Rules reference

The pd2af transformation is driven by a set of rules (encoded in ASP). Every rule is language-agnostic (a base rule) or specific to an input language (a variant rule, for CellDesigner or SBGN PD). Rules are organized in groups, each representing a coherent functional unit — the whole a --exclude-group can drop. Every group id reads <family>:<member>, and the family is the coarse concern the group addresses.

This page is generated from the live registry in pd2af.asp.rules. It presents a by-mode view of which rules each mode uses, a canonical reference documenting each rule once, and an alphabetical index of every rule.

By mode

Within a mode a group is excludable (nothing else the mode includes depends on it, so --exclude-group can drop it cleanly) or mandatory (another included group depends on it, directly or by filling a slot it requires). The same group can be excludable in one mode and mandatory in another.

`normal`

activity:core (mandatory)

Mandatory activity machinery: the candidate->activity bridge and the two global toggles.

Rule	Variant
`activity:core:from_candidate`
`activity:core:from_global_suppress`
`activity:core:celldesigner:from_global_activate`	CellDesigner
`activity:core:sbgn_pd:from_global_activate`	SBGN PD

activity:phenotype (excludable)

Excludable: a phenotype is an activity candidate (reason isPhenotype).

Rule	Variant
`activity:phenotype:from_phenotype`

activity:active_marker (mandatory)

Excludable: an explicit active marker makes a species/entity pool an activity candidate (CellDesigner: hasActive flag or active structural state; SBGN-PD: active state variable, including on subunits).

Rule	Variant
`activity:active_marker:celldesigner:from_active_flag`	CellDesigner
`activity:active_marker:celldesigner:from_active_structural_state`	CellDesigner
`activity:active_marker:sbgn_pd:from_active_state_variable`	SBGN PD
`activity:active_marker:sbgn_pd:from_active_subunit_state_variable`	SBGN PD

activity:modulation_source (excludable)

Excludable: the source of a modulation arc (CellDesigner: a modulation arc or a reaction modifier, which in SBGN-PD folds into the same arc-to-process case) is an activity candidate.

Rule	Variant
`activity:modulation_source:celldesigner:from_modulation_source`	CellDesigner
`activity:modulation_source:celldesigner:from_reaction_modulator`	CellDesigner
`activity:modulation_source:sbgn_pd:from_modulation_source`	SBGN PD

activity:gate_input (excludable)

Excludable: an input feeding a boolean logic gate / logical operator is an activity candidate (reason isGateInput).

Rule	Variant
`activity:gate_input:celldesigner:from_gate_input`	CellDesigner
`activity:gate_input:sbgn_pd:from_operator_input`	SBGN PD

topology:core (mandatory)

Mode-agnostic structural helpers shared by every mode: isSubunit, hasActiveDescendantSubunit.

Rule	Variant
`topology:core:is_subunit`
`topology:core:has_active_descendant_direct`
`topology:core:has_active_descendant_transitive`

topology:top_level (mandatory)

Resolves every species to its outermost top-level entity: a non-subunit resolves to itself; a subunit -- at any nesting depth -- resolves to the outermost complex that contains it.

Rule	Variant
`topology:top_level:recursive`
`topology:top_level:celldesigner:self`	CellDesigner
`topology:top_level:sbgn_pd:self`	SBGN PD
`topology:top_level:sbgn_pd:phenotype_self`	SBGN PD

preparation:complex (mandatory)

The complex-keeping modes (normal, keep-reactions) key a species with activity by the keptSpeciesKey of its top-level entity (the topology:top_level group): itself when top-level, its outermost complex when a subunit.

Rule	Variant
`preparation:complex:key`
`preparation:complex:celldesigner:carrier`	CellDesigner
`preparation:complex:sbgn_pd:carrier_entity_pool`	SBGN PD
`preparation:complex:sbgn_pd:carrier_phenotype`	SBGN PD

paths:core (mandatory)

Builds the direct (single-hop) kinded propagatesInfluence(SOURCE_SPECIES, TARGET_SPECIES, INFLUENCE_KIND) relation from PD reactions and modulation arcs, plus the production-cycle relations that gate transitive extension.

Rule	Variant
`paths:core:is_transformed_to`
`paths:core:is_cyclically_transformed_to`
`paths:core:composes_to`
`paths:core:celldesigner:catalyzer_to_product`	CellDesigner
`paths:core:celldesigner:physical_stimulator_to_product`	CellDesigner
`paths:core:celldesigner:trigger_to_product`	CellDesigner
`paths:core:celldesigner:modulation_arc_influence`	CellDesigner
`paths:core:celldesigner:inhibitor_to_product`	CellDesigner
`paths:core:celldesigner:modulator_to_product`	CellDesigner
`paths:core:celldesigner:unknown_catalyzer_to_product`	CellDesigner
`paths:core:celldesigner:unknown_inhibitor_to_product`	CellDesigner
`paths:core:celldesigner:is_directly_transformed_to`	CellDesigner
`paths:core:sbgn_pd:modulation_to_product`	SBGN PD
`paths:core:sbgn_pd:modulation_to_phenotype`	SBGN PD
`paths:core:sbgn_pd:is_directly_transformed_to`	SBGN PD

paths:chaining (excludable)

Excludable multi-hop transitivity: extends a propagatesInfluence path through one more reactant->product hop (a reaction in CellDesigner, a process in SBGN-PD), carrying the kind via composesTo (triggering degrades to positivelyInfluences) and refusing to extend across a hop inside a production cycle (not isCyclicallyTransformedTo).

Rule	Variant
`paths:chaining:celldesigner:transitive_through_reaction`	CellDesigner
`paths:chaining:sbgn_pd:transitive_through_process`	SBGN PD

entity:identity (mandatory)

When two elements are the same entity in different states: isSameEntityAs(ELEMENT, OTHER_ELEMENT) holds for two species sharing a template (protein, gene, RNA reference), and for two template-free elements of the same kind and name (CellDesigner) or label (SBGN-PD).

Rule	Variant
`entity:identity:celldesigner:from_template`	CellDesigner
`entity:identity:celldesigner:kind`	CellDesigner
`entity:identity:celldesigner:from_name`	CellDesigner
`entity:identity:sbgn_pd:kind`	SBGN PD
`entity:identity:sbgn_pd:from_label`	SBGN PD

influences:kind (mandatory)

Maps each modulation arc to its influence kind via hasInfluenceKind(MODULATION, INFLUENCE_KIND), the single place the arc-type->kind knowledge lives.

Rule	Variant
`influences:kind:celldesigner:catalysis`	CellDesigner
`influences:kind:celldesigner:physical_stimulation`	CellDesigner
`influences:kind:celldesigner:positive_influence`	CellDesigner
`influences:kind:celldesigner:triggering`	CellDesigner
`influences:kind:celldesigner:inhibition`	CellDesigner
`influences:kind:celldesigner:negative_influence`	CellDesigner
`influences:kind:celldesigner:modulation`	CellDesigner
`influences:kind:celldesigner:unknown_catalysis`	CellDesigner
`influences:kind:celldesigner:unknown_physical_stimulation`	CellDesigner
`influences:kind:celldesigner:unknown_positive_influence`	CellDesigner
`influences:kind:celldesigner:unknown_triggering`	CellDesigner
`influences:kind:celldesigner:unknown_inhibition`	CellDesigner
`influences:kind:celldesigner:unknown_negative_influence`	CellDesigner
`influences:kind:celldesigner:unknown_modulation`	CellDesigner
`influences:kind:sbgn_pd:necessary_stimulation`	SBGN PD
`influences:kind:sbgn_pd:stimulation`	SBGN PD
`influences:kind:sbgn_pd:inhibition`	SBGN PD
`influences:kind:sbgn_pd:modulation`	SBGN PD

influences:core (excludable)

Derivation: emits new(activity(KEY)) for every activity key, and lifts every kinded path into the internal influences(SOURCE_KEY, TARGET_KEY, INFLUENCE_KIND) relation by resolving both endpoints through their activity carrier and key.

Rule	Variant
`influences:core:activity`
`influences:core:path`

influences:consumption (excludable)

Excludable consumption/sparing reasoning: a reaction depletes its reactants, so a modifier that drives the reaction also acts on every reactant that is itself an activity -- catalyzer/physicalStimulator/trigger negatively influence each consumed reactant, inhibitor positively influences each spared reactant, and the unknown modifiers contribute the unknown twins.

Rule	Variant
`influences:consumption:returns_reactant_as_activity`
`influences:consumption:celldesigner:catalyzer_consumes_reactant`	CellDesigner
`influences:consumption:celldesigner:physical_stimulator_consumes_reactant`	CellDesigner
`influences:consumption:celldesigner:trigger_consumes_reactant`	CellDesigner
`influences:consumption:celldesigner:inhibitor_spares_reactant`	CellDesigner
`influences:consumption:celldesigner:unknown_catalyzer_consumes_reactant`	CellDesigner
`influences:consumption:celldesigner:unknown_inhibitor_spares_reactant`	CellDesigner
`influences:consumption:sbgn_pd:stimulation_consumes_reactant`	SBGN PD
`influences:consumption:sbgn_pd:inhibition_spares_reactant`	SBGN PD

influences:binding_activation (excludable)

Excludable activation-by-binding reasoning: when a reaction turns an entity drawn inactive as a reactant (or inside a reactant complex) into an active subunit of a product complex, the binding activated it, so every other reactant of that reaction -- one that is neither the same entity nor itself activated by the same reaction -- becomes an activity (reason isBindingActivator) and positively influences the activity carrying the active subunit: its top-level complex in normal, the promoted subunit in no-complex.

Rule	Variant
`influences:binding_activation:is_descendant_subunit_of`
`influences:binding_activation:is_self_or_descendant_subunit_of`
`influences:binding_activation:active_marker_from_override`
`influences:binding_activation:activates_by_binding`
`influences:binding_activation:contains_inactive_reactant_of`
`influences:binding_activation:is_binding_activator_of`
`influences:binding_activation:candidate`
`influences:binding_activation:influence`
`influences:binding_activation:celldesigner:active_marker_from_active_flag`	CellDesigner
`influences:binding_activation:celldesigner:active_marker_from_structural_state`	CellDesigner
`influences:binding_activation:sbgn_pd:active_marker_from_state_variable`	SBGN PD

influences:output (excludable)

Shared fan-out from the internal influences(SOURCE, TARGET, INFLUENCE_KIND) relation to the typed new(...) influence heads — one rule per kind.

Rule	Variant
`influences:output:positive`
`influences:output:negative`
`influences:output:modulation`
`influences:output:triggering`
`influences:output:unknown_positive`
`influences:output:unknown_negative`
`influences:output:unknown_modulation`
`influences:output:unknown_triggering`

gates:core (excludable)

Authored logical operators (CellDesigner BooleanLogicGate, SBGN-PD LogicalOperator): emits the operator node (logicalOperator/2, token-typed), its input edges (logicalOperatorInput/2, each input resolved through carrier/key -- or, for SBGN-PD, through the referred operator's own key when the input refers to another logical operator), and the operator-sourced influence written straight into the internal influences/3 relation by reusing the existing propagatesInfluence(OPERATOR, TARGET, INFLUENCE_KIND) closure.

Rule	Variant
`gates:core:celldesigner:node_and`	CellDesigner
`gates:core:celldesigner:node_or`	CellDesigner
`gates:core:celldesigner:node_not`	CellDesigner
`gates:core:celldesigner:node_unknown`	CellDesigner
`gates:core:celldesigner:input_edge`	CellDesigner
`gates:core:celldesigner:influence`	CellDesigner
`gates:core:sbgn_pd:node_and`	SBGN PD
`gates:core:sbgn_pd:node_or`	SBGN PD
`gates:core:sbgn_pd:node_not`	SBGN PD
`gates:core:sbgn_pd:input_edge`	SBGN PD
`gates:core:sbgn_pd:input_edge_operator`	SBGN PD
`gates:core:sbgn_pd:influence`	SBGN PD

`no-complex`

activity:core (mandatory)

Mandatory activity machinery: the candidate->activity bridge and the two global toggles.

Rule	Variant
`activity:core:from_candidate`
`activity:core:from_global_suppress`
`activity:core:celldesigner:from_global_activate`	CellDesigner
`activity:core:sbgn_pd:from_global_activate`	SBGN PD

activity:phenotype (excludable)

Excludable: a phenotype is an activity candidate (reason isPhenotype).

Rule	Variant
`activity:phenotype:from_phenotype`

activity:active_marker (mandatory)

Excludable: an explicit active marker makes a species/entity pool an activity candidate (CellDesigner: hasActive flag or active structural state; SBGN-PD: active state variable, including on subunits).

Rule	Variant
`activity:active_marker:celldesigner:from_active_flag`	CellDesigner
`activity:active_marker:celldesigner:from_active_structural_state`	CellDesigner
`activity:active_marker:sbgn_pd:from_active_state_variable`	SBGN PD
`activity:active_marker:sbgn_pd:from_active_subunit_state_variable`	SBGN PD

activity:modulation_source (excludable)

Excludable: the source of a modulation arc (CellDesigner: a modulation arc or a reaction modifier, which in SBGN-PD folds into the same arc-to-process case) is an activity candidate.

Rule	Variant
`activity:modulation_source:celldesigner:from_modulation_source`	CellDesigner
`activity:modulation_source:celldesigner:from_reaction_modulator`	CellDesigner
`activity:modulation_source:sbgn_pd:from_modulation_source`	SBGN PD

activity:gate_input (excludable)

Excludable: an input feeding a boolean logic gate / logical operator is an activity candidate (reason isGateInput).

Rule	Variant
`activity:gate_input:celldesigner:from_gate_input`	CellDesigner
`activity:gate_input:sbgn_pd:from_operator_input`	SBGN PD

topology:core (mandatory)

Mode-agnostic structural helpers shared by every mode: isSubunit, hasActiveDescendantSubunit.

Rule	Variant
`topology:core:is_subunit`
`topology:core:has_active_descendant_direct`
`topology:core:has_active_descendant_transitive`

preparation:no_complex (mandatory)

The complex-dissolving mode (no-complex): a complex with any (transitive) active descendant is deleted; a non-deleted top-level species with activity is keyed by keptSpeciesKey(SELF); a subunit of a deleted complex is promoted to top level, keyed by promotedSubunitKey(SELF) (paths reach it via paths:complex_traversal).

Rule	Variant
`preparation:no_complex:deleted`
`preparation:no_complex:subunit_of_deleted_direct`
`preparation:no_complex:subunit_of_deleted_transitive`
`preparation:no_complex:key_top_level`
`preparation:no_complex:key_promoted_subunit`
`preparation:no_complex:celldesigner:carrier`	CellDesigner
`preparation:no_complex:sbgn_pd:carrier_entity_pool`	SBGN PD
`preparation:no_complex:sbgn_pd:carrier_phenotype`	SBGN PD
`preparation:no_complex:sbgn_pd:carrier_subunit`	SBGN PD

paths:core (mandatory)

Builds the direct (single-hop) kinded propagatesInfluence(SOURCE_SPECIES, TARGET_SPECIES, INFLUENCE_KIND) relation from PD reactions and modulation arcs, plus the production-cycle relations that gate transitive extension.

Rule	Variant
`paths:core:is_transformed_to`
`paths:core:is_cyclically_transformed_to`
`paths:core:composes_to`
`paths:core:celldesigner:catalyzer_to_product`	CellDesigner
`paths:core:celldesigner:physical_stimulator_to_product`	CellDesigner
`paths:core:celldesigner:trigger_to_product`	CellDesigner
`paths:core:celldesigner:modulation_arc_influence`	CellDesigner
`paths:core:celldesigner:inhibitor_to_product`	CellDesigner
`paths:core:celldesigner:modulator_to_product`	CellDesigner
`paths:core:celldesigner:unknown_catalyzer_to_product`	CellDesigner
`paths:core:celldesigner:unknown_inhibitor_to_product`	CellDesigner
`paths:core:celldesigner:is_directly_transformed_to`	CellDesigner
`paths:core:sbgn_pd:modulation_to_product`	SBGN PD
`paths:core:sbgn_pd:modulation_to_phenotype`	SBGN PD
`paths:core:sbgn_pd:is_directly_transformed_to`	SBGN PD

paths:chaining (excludable)

Excludable multi-hop transitivity: extends a propagatesInfluence path through one more reactant->product hop (a reaction in CellDesigner, a process in SBGN-PD), carrying the kind via composesTo (triggering degrades to positivelyInfluences) and refusing to extend across a hop inside a production cycle (not isCyclicallyTransformedTo).

Rule	Variant
`paths:chaining:celldesigner:transitive_through_reaction`	CellDesigner
`paths:chaining:sbgn_pd:transitive_through_process`	SBGN PD

paths:complex_traversal (excludable)

Extends paths through complex containment for the no-complex mode: a path touching a complex is propagated to/from each of its subunits so influences reach the surviving subunit activities.

Rule	Variant
`paths:complex_traversal:into_subunits`
`paths:complex_traversal:from_subunits`

entity:identity (mandatory)

When two elements are the same entity in different states: isSameEntityAs(ELEMENT, OTHER_ELEMENT) holds for two species sharing a template (protein, gene, RNA reference), and for two template-free elements of the same kind and name (CellDesigner) or label (SBGN-PD).

Rule	Variant
`entity:identity:celldesigner:from_template`	CellDesigner
`entity:identity:celldesigner:kind`	CellDesigner
`entity:identity:celldesigner:from_name`	CellDesigner
`entity:identity:sbgn_pd:kind`	SBGN PD
`entity:identity:sbgn_pd:from_label`	SBGN PD

influences:kind (mandatory)

Maps each modulation arc to its influence kind via hasInfluenceKind(MODULATION, INFLUENCE_KIND), the single place the arc-type->kind knowledge lives.

Rule	Variant
`influences:kind:celldesigner:catalysis`	CellDesigner
`influences:kind:celldesigner:physical_stimulation`	CellDesigner
`influences:kind:celldesigner:positive_influence`	CellDesigner
`influences:kind:celldesigner:triggering`	CellDesigner
`influences:kind:celldesigner:inhibition`	CellDesigner
`influences:kind:celldesigner:negative_influence`	CellDesigner
`influences:kind:celldesigner:modulation`	CellDesigner
`influences:kind:celldesigner:unknown_catalysis`	CellDesigner
`influences:kind:celldesigner:unknown_physical_stimulation`	CellDesigner
`influences:kind:celldesigner:unknown_positive_influence`	CellDesigner
`influences:kind:celldesigner:unknown_triggering`	CellDesigner
`influences:kind:celldesigner:unknown_inhibition`	CellDesigner
`influences:kind:celldesigner:unknown_negative_influence`	CellDesigner
`influences:kind:celldesigner:unknown_modulation`	CellDesigner
`influences:kind:sbgn_pd:necessary_stimulation`	SBGN PD
`influences:kind:sbgn_pd:stimulation`	SBGN PD
`influences:kind:sbgn_pd:inhibition`	SBGN PD
`influences:kind:sbgn_pd:modulation`	SBGN PD

influences:core (excludable)

Derivation: emits new(activity(KEY)) for every activity key, and lifts every kinded path into the internal influences(SOURCE_KEY, TARGET_KEY, INFLUENCE_KIND) relation by resolving both endpoints through their activity carrier and key.

Rule	Variant
`influences:core:activity`
`influences:core:path`

influences:consumption (excludable)

Excludable consumption/sparing reasoning: a reaction depletes its reactants, so a modifier that drives the reaction also acts on every reactant that is itself an activity -- catalyzer/physicalStimulator/trigger negatively influence each consumed reactant, inhibitor positively influences each spared reactant, and the unknown modifiers contribute the unknown twins.

Rule	Variant
`influences:consumption:returns_reactant_as_activity`
`influences:consumption:celldesigner:catalyzer_consumes_reactant`	CellDesigner
`influences:consumption:celldesigner:physical_stimulator_consumes_reactant`	CellDesigner
`influences:consumption:celldesigner:trigger_consumes_reactant`	CellDesigner
`influences:consumption:celldesigner:inhibitor_spares_reactant`	CellDesigner
`influences:consumption:celldesigner:unknown_catalyzer_consumes_reactant`	CellDesigner
`influences:consumption:celldesigner:unknown_inhibitor_spares_reactant`	CellDesigner
`influences:consumption:sbgn_pd:stimulation_consumes_reactant`	SBGN PD
`influences:consumption:sbgn_pd:inhibition_spares_reactant`	SBGN PD

influences:binding_activation (excludable)

Excludable activation-by-binding reasoning: when a reaction turns an entity drawn inactive as a reactant (or inside a reactant complex) into an active subunit of a product complex, the binding activated it, so every other reactant of that reaction -- one that is neither the same entity nor itself activated by the same reaction -- becomes an activity (reason isBindingActivator) and positively influences the activity carrying the active subunit: its top-level complex in normal, the promoted subunit in no-complex.

Rule	Variant
`influences:binding_activation:is_descendant_subunit_of`
`influences:binding_activation:is_self_or_descendant_subunit_of`
`influences:binding_activation:active_marker_from_override`
`influences:binding_activation:activates_by_binding`
`influences:binding_activation:contains_inactive_reactant_of`
`influences:binding_activation:is_binding_activator_of`
`influences:binding_activation:candidate`
`influences:binding_activation:influence`
`influences:binding_activation:celldesigner:active_marker_from_active_flag`	CellDesigner
`influences:binding_activation:celldesigner:active_marker_from_structural_state`	CellDesigner
`influences:binding_activation:sbgn_pd:active_marker_from_state_variable`	SBGN PD

influences:output (excludable)

Shared fan-out from the internal influences(SOURCE, TARGET, INFLUENCE_KIND) relation to the typed new(...) influence heads — one rule per kind.

Rule	Variant
`influences:output:positive`
`influences:output:negative`
`influences:output:modulation`
`influences:output:triggering`
`influences:output:unknown_positive`
`influences:output:unknown_negative`
`influences:output:unknown_modulation`
`influences:output:unknown_triggering`

gates:core (excludable)

Authored logical operators (CellDesigner BooleanLogicGate, SBGN-PD LogicalOperator): emits the operator node (logicalOperator/2, token-typed), its input edges (logicalOperatorInput/2, each input resolved through carrier/key -- or, for SBGN-PD, through the referred operator's own key when the input refers to another logical operator), and the operator-sourced influence written straight into the internal influences/3 relation by reusing the existing propagatesInfluence(OPERATOR, TARGET, INFLUENCE_KIND) closure.

Rule	Variant
`gates:core:celldesigner:node_and`	CellDesigner
`gates:core:celldesigner:node_or`	CellDesigner
`gates:core:celldesigner:node_not`	CellDesigner
`gates:core:celldesigner:node_unknown`	CellDesigner
`gates:core:celldesigner:input_edge`	CellDesigner
`gates:core:celldesigner:influence`	CellDesigner
`gates:core:sbgn_pd:node_and`	SBGN PD
`gates:core:sbgn_pd:node_or`	SBGN PD
`gates:core:sbgn_pd:node_not`	SBGN PD
`gates:core:sbgn_pd:input_edge`	SBGN PD
`gates:core:sbgn_pd:input_edge_operator`	SBGN PD
`gates:core:sbgn_pd:influence`	SBGN PD

`keep-reactions`

activity:core (mandatory)

Mandatory activity machinery: the candidate->activity bridge and the two global toggles.

Rule	Variant
`activity:core:from_candidate`
`activity:core:from_global_suppress`
`activity:core:celldesigner:from_global_activate`	CellDesigner
`activity:core:sbgn_pd:from_global_activate`	SBGN PD

topology:core (mandatory)

Mode-agnostic structural helpers shared by every mode: isSubunit, hasActiveDescendantSubunit.

Rule	Variant
`topology:core:is_subunit`
`topology:core:has_active_descendant_direct`
`topology:core:has_active_descendant_transitive`

topology:top_level (mandatory)

Resolves every species to its outermost top-level entity: a non-subunit resolves to itself; a subunit -- at any nesting depth -- resolves to the outermost complex that contains it.

Rule	Variant
`topology:top_level:recursive`
`topology:top_level:celldesigner:self`	CellDesigner
`topology:top_level:sbgn_pd:self`	SBGN PD
`topology:top_level:sbgn_pd:phenotype_self`	SBGN PD

preparation:complex (mandatory)

The complex-keeping modes (normal, keep-reactions) key a species with activity by the keptSpeciesKey of its top-level entity (the topology:top_level group): itself when top-level, its outermost complex when a subunit.

Rule	Variant
`preparation:complex:key`
`preparation:complex:celldesigner:carrier`	CellDesigner
`preparation:complex:sbgn_pd:carrier_entity_pool`	SBGN PD
`preparation:complex:sbgn_pd:carrier_phenotype`	SBGN PD

paths:core (mandatory)

Builds the direct (single-hop) kinded propagatesInfluence(SOURCE_SPECIES, TARGET_SPECIES, INFLUENCE_KIND) relation from PD reactions and modulation arcs, plus the production-cycle relations that gate transitive extension.

Rule	Variant
`paths:core:is_transformed_to`
`paths:core:is_cyclically_transformed_to`
`paths:core:composes_to`
`paths:core:celldesigner:catalyzer_to_product`	CellDesigner
`paths:core:celldesigner:physical_stimulator_to_product`	CellDesigner
`paths:core:celldesigner:trigger_to_product`	CellDesigner
`paths:core:celldesigner:modulation_arc_influence`	CellDesigner
`paths:core:celldesigner:inhibitor_to_product`	CellDesigner
`paths:core:celldesigner:modulator_to_product`	CellDesigner
`paths:core:celldesigner:unknown_catalyzer_to_product`	CellDesigner
`paths:core:celldesigner:unknown_inhibitor_to_product`	CellDesigner
`paths:core:celldesigner:is_directly_transformed_to`	CellDesigner
`paths:core:sbgn_pd:modulation_to_product`	SBGN PD
`paths:core:sbgn_pd:modulation_to_phenotype`	SBGN PD
`paths:core:sbgn_pd:is_directly_transformed_to`	SBGN PD

influences:kind (mandatory)

Maps each modulation arc to its influence kind via hasInfluenceKind(MODULATION, INFLUENCE_KIND), the single place the arc-type->kind knowledge lives.

Rule	Variant
`influences:kind:celldesigner:catalysis`	CellDesigner
`influences:kind:celldesigner:physical_stimulation`	CellDesigner
`influences:kind:celldesigner:positive_influence`	CellDesigner
`influences:kind:celldesigner:triggering`	CellDesigner
`influences:kind:celldesigner:inhibition`	CellDesigner
`influences:kind:celldesigner:negative_influence`	CellDesigner
`influences:kind:celldesigner:modulation`	CellDesigner
`influences:kind:celldesigner:unknown_catalysis`	CellDesigner
`influences:kind:celldesigner:unknown_physical_stimulation`	CellDesigner
`influences:kind:celldesigner:unknown_positive_influence`	CellDesigner
`influences:kind:celldesigner:unknown_triggering`	CellDesigner
`influences:kind:celldesigner:unknown_inhibition`	CellDesigner
`influences:kind:celldesigner:unknown_negative_influence`	CellDesigner
`influences:kind:celldesigner:unknown_modulation`	CellDesigner
`influences:kind:sbgn_pd:necessary_stimulation`	SBGN PD
`influences:kind:sbgn_pd:stimulation`	SBGN PD
`influences:kind:sbgn_pd:inhibition`	SBGN PD
`influences:kind:sbgn_pd:modulation`	SBGN PD

influences:core (mandatory)

Derivation: emits new(activity(KEY)) for every activity key, and lifts every kinded path into the internal influences(SOURCE_KEY, TARGET_KEY, INFLUENCE_KIND) relation by resolving both endpoints through their activity carrier and key.

Rule	Variant
`influences:core:activity`
`influences:core:path`

influences:output (excludable)

Shared fan-out from the internal influences(SOURCE, TARGET, INFLUENCE_KIND) relation to the typed new(...) influence heads — one rule per kind.

Rule	Variant
`influences:output:positive`
`influences:output:negative`
`influences:output:modulation`
`influences:output:triggering`
`influences:output:unknown_positive`
`influences:output:unknown_negative`
`influences:output:unknown_modulation`
`influences:output:unknown_triggering`

gates:core (excludable)

Authored logical operators (CellDesigner BooleanLogicGate, SBGN-PD LogicalOperator): emits the operator node (logicalOperator/2, token-typed), its input edges (logicalOperatorInput/2, each input resolved through carrier/key -- or, for SBGN-PD, through the referred operator's own key when the input refers to another logical operator), and the operator-sourced influence written straight into the internal influences/3 relation by reusing the existing propagatesInfluence(OPERATOR, TARGET, INFLUENCE_KIND) closure.

Rule	Variant
`gates:core:celldesigner:node_and`	CellDesigner
`gates:core:celldesigner:node_or`	CellDesigner
`gates:core:celldesigner:node_not`	CellDesigner
`gates:core:celldesigner:node_unknown`	CellDesigner
`gates:core:celldesigner:input_edge`	CellDesigner
`gates:core:celldesigner:influence`	CellDesigner
`gates:core:sbgn_pd:node_and`	SBGN PD
`gates:core:sbgn_pd:node_or`	SBGN PD
`gates:core:sbgn_pd:node_not`	SBGN PD
`gates:core:sbgn_pd:input_edge`	SBGN PD
`gates:core:sbgn_pd:input_edge_operator`	SBGN PD
`gates:core:sbgn_pd:influence`	SBGN PD

keep_reactions:activity (excludable)

The keep-reactions premise that every species is an activity, replacing the structural-reason activity:* feature-groups (each of which is inert once every species is a candidate, so the mode omits them).

Rule	Variant
`keep_reactions:activity:from_species`

keep_reactions:influences (excludable)

The keep-reactions premise that every reaction is kept: each (reactant, product) pair of a reaction becomes one positive influence.

Rule	Variant
`keep_reactions:influences:reactant_to_product`

Rule groups

`activity`

`activity:core`

Mandatory activity machinery: the candidate->activity bridge and the two global toggles. A single bridging rule promotes a hasActivityCandidate(ELEMENT, REASON) to hasActivity unless the element is suppressActivity (the --set-inactive veto). globalSuppress (--set-all-inactive) suppresses every candidate except those the solver marked forceActive (the per-id --set-active override), realising the precedence per-id > global > rules; globalActivate (--set-all-active) turns every top-level species/entity pool into a candidate. Every activity feature-group and every downstream group depends on this, so the dependency graph forbids excluding it -- the global toggles stay wired to their CLI flags. The structural-reason rules (phenotype, active marker, modulation source, gate input) live in the excludable activity:* feature-groups.

Rule	Variant	Documentation
`activity:core:from_candidate`		An activity candidate becomes an actual activity unless it has been vetoed. This is the single interception point for the `--set-inactive` veto (the `suppressActivity` marker; blanket suppression, so it also blocks the `--set-active` `isInputParameter` candidate, which is injected as a candidate). All downstream body references key on `hasActivity`, so they automatically respect suppression.
`activity:core:from_global_suppress`		The set-all-inactive toggle suppresses every activity candidate, except those pinned active per id. This realises the precedence per-id > global > rules for the inactive toggle: `globalSuppress` (`--set-all-inactive`) blankets everything, and `forceActive` (the per-id `--set-active` override) carves out the exceptions. It keys on `hasActivityCandidate`, so it also silences subunit-derived candidates (subunits are suppressed under `--set-all-inactive`).
`activity:core:celldesigner:from_global_activate`	CellDesigner	Under the set-all-active toggle, every top-level species is an activity candidate. It fires with reason `isGlobalActive` when `globalActivate` (`--set-all-active`) is set. The `not hasSubunit(_, SPECIES)` guard excludes subunits (in CellDesigner a subunit is a species): a subunit is a structural component of its complex, never a top-level activity, so the toggle activates the complex, not its parts. This is the subunit asymmetry -- subunits are not activated under `--set-all-active`, though they are suppressed under `--set-all-inactive`.
`activity:core:sbgn_pd:from_global_activate`	SBGN PD	Under the set-all-active toggle, every entity pool is an activity candidate. It fires with reason `isGlobalActive` when `globalActivate` (`--set-all-active`) is set -- the SBGN PD parallel of CellDesigner's global-activate rule. No `not hasSubunit` guard is needed: in SBGN PD a subunit is an `SBGNAuxiliaryUnit`, not an `entityPool`, so the `entityPool` guard already excludes subunits. This preserves the subunit asymmetry -- subunits are not activated under `--set-all-active`.

`activity:phenotype`

Excludable: a phenotype is an activity candidate (reason isPhenotype). Exclude with --exclude-group activity:phenotype to stop treating phenotypes as activities.

Rule	Variant	Documentation
`activity:phenotype:from_phenotype`		A phenotype is always an activity candidate. Both languages emit the `phenotype` signal, so this rule is shared; it fires with reason `isPhenotype`.

`activity:active_marker`

Excludable: an explicit active marker makes a species/entity pool an activity candidate (CellDesigner: hasActive flag or active structural state; SBGN-PD: active state variable, including on subunits). Exclude with --exclude-group activity:active_marker.

Rule	Variant	Documentation
`activity:active_marker:celldesigner:from_active_flag`	CellDesigner	A species explicitly marked as active is an activity candidate. This fires when its `hasActive` flag is 1 (reason `isActive`).
`activity:active_marker:celldesigner:from_active_structural_state`	CellDesigner	A species in an active structural state is an activity candidate. This fires when it carries a structural state whose value is "active" (reason `hasActiveStructuralState`).
`activity:active_marker:sbgn_pd:from_active_state_variable`	SBGN PD	An entity pool in an active state is an activity candidate. This fires when it carries a state variable whose value is "active" (reason `hasActiveStateVariable`) -- the SBGN PD parallel of CellDesigner's active structural state.
`activity:active_marker:sbgn_pd:from_active_subunit_state_variable`	SBGN PD	A subunit in an active state is an activity candidate. This fires when the subunit carries a state variable whose value is "active". Its complex therefore inherits activity, and in the `no-complex` mode the subunit can be promoted. It is the parallel of CellDesigner, where subunits are species and so the active-structural-state rule already covers them.

`activity:modulation_source`

Excludable: the source of a modulation arc (CellDesigner: a modulation arc or a reaction modifier, which in SBGN-PD folds into the same arc-to-process case) is an activity candidate. Exclude with --exclude-group activity:modulation_source.

Rule	Variant	Documentation
`activity:modulation_source:celldesigner:from_modulation_source`	CellDesigner	A species that is the source of a modulation arc is an activity candidate. This covers both known and unknown modulations that have some target (reason `isModulationSource`); keying on `knownOrUnknownModulation` rather than `modulation` is what lets the source of an unknown modulation become an activity node.
`activity:modulation_source:celldesigner:from_reaction_modulator`	CellDesigner	A species that modulates a reaction is an activity candidate. This fires when the species is referred to by a reaction modulator, known or unknown, that modifies some target reaction (reason `isReactionModulator`); keying on `knownOrUnknownModulator` rather than `modulator` is what lets an unknown catalyzer/inhibitor become an activity node.
`activity:modulation_source:sbgn_pd:from_modulation_source`	SBGN PD	An entity pool that is the source of a modulation arc is an activity candidate. This fires when the arc's target is a process (reason `isModulationSource`) and is the SBGN PD parallel of both the CellDesigner modulation-arc and reaction-modifier rules.

`activity:gate_input`

Excludable: an input feeding a boolean logic gate / logical operator is an activity candidate (reason isGateInput). Exclude with --exclude-group activity:gate_input.

Rule	Variant	Documentation
`activity:gate_input:celldesigner:from_gate_input`	CellDesigner	A species feeding a boolean logic gate is an activity candidate. It fires with reason `isGateInput`. A gate is structurally always an influence/modulation source or reaction modifier, so each of its inputs is an active driver of the downstream target -- a semantic guarantee, not a fallback. The element is activated regardless of kind (species, complex, ion, ...); the carrier rules route each kind. `hasReferredElement` in CellDesigner only relates a gate input to its species, so no extra guard is needed.
`activity:gate_input:sbgn_pd:from_operator_input`	SBGN PD	An entity pool feeding a logical operator is an activity candidate. It fires with reason `isGateInput` -- the SBGN PD parallel of CellDesigner's gate-input activation. The `entityPool` guard excludes the deferred nested-operator case: an operator feeding another operator has no activity carrier, so such an input simply dangles. In SBGN PD `hasReferredElement` relates many roles (reactant, product, modulation participant) to entities, so both the `logicalOperatorInput` and `entityPool` guards are needed.

`topology`

`topology:core`

Mode-agnostic structural helpers shared by every mode: isSubunit, hasActiveDescendantSubunit.

Rule	Variant	Documentation
`topology:core:is_subunit`		A species is a subunit if it appears on the right side of any `hasSubunit` relation.
`topology:core:has_active_descendant_direct`		A complex has an active descendant if any direct subunit has activity.
`topology:core:has_active_descendant_transitive`		The `hasActiveDescendantSubunit` relation is transitive through complex containment.

`topology:top_level`

Resolves every species to its outermost top-level entity: a non-subunit resolves to itself; a subunit -- at any nesting depth -- resolves to the outermost complex that contains it. The complex-keeping modes (normal, keep-reactions) key a species by its top-level entity, so a subunit is never its own activity and its influences attach to its top-level complex (a subunit is a structural component, not an independent influencer).

Rule	Variant	Documentation
`topology:top_level:recursive`		A subunit resolves to the same top-level entity as its parent complex, recursively through nested complexes -- so a subunit at any depth resolves to its outermost complex.
`topology:top_level:celldesigner:self`	CellDesigner	CellDesigner: a species that is not a subunit of any complex is its own top-level entity.
`topology:top_level:sbgn_pd:self`	SBGN PD	SBGN-PD: an entity pool that is not a subunit of any complex is its own top-level entity.
`topology:top_level:sbgn_pd:phenotype_self`	SBGN PD	SBGN-PD: a phenotype is a process, not an entity pool, so the entity-pool self-rule never keys it; a phenotype is never a subunit, so it is always its own top-level entity. Without this an SBGN phenotype gets `hasActivity` but no activity key and is silently dropped from `normal` output. The `no-complex` mode keys via `not isSubunit`/`not delete` and already include phenotypes; CellDesigner phenotypes are species (covered by the species self-rule).

`preparation`

`preparation:complex`

The complex-keeping modes (normal, keep-reactions) key a species with activity by the keptSpeciesKey of its top-level entity (the topology:top_level group): itself when top-level, its outermost complex when a subunit. A subunit therefore contributes no activity of its own -- it is a structural component of its complex, and any influence it carries attaches to the top-level complex (the active descendant directly keys the complex, so the assembly is represented without a separate inherit-activity rule). Carriers are identity; the rerouting lives entirely in the key. The keep_species option bears on the build stage alone, where it decides whether the PTM decorations are stripped and the content-equal results merged.

Rule	Variant	Documentation
`preparation:complex:key`		A species with activity is keyed by the `keptSpeciesKey` of its top-level entity (itself when top-level; its outermost complex when a subunit).
`preparation:complex:celldesigner:carrier`	CellDesigner	Each species is its own activity carrier (no rerouting; a subunit endpoint is rerouted to its top-level complex by the `topology:top_level` key, not by the carrier).
`preparation:complex:sbgn_pd:carrier_entity_pool`	SBGN PD	SBGN-PD: each entity pool is its own activity carrier.
`preparation:complex:sbgn_pd:carrier_phenotype`	SBGN PD	SBGN-PD: each phenotype process is its own activity carrier (phenotypes are activities, not entity pools).

`preparation:no_complex`

The complex-dissolving mode (no-complex): a complex with any (transitive) active descendant is deleted; a non-deleted top-level species with activity is keyed by keptSpeciesKey(SELF); a subunit of a deleted complex is promoted to top level, keyed by promotedSubunitKey(SELF) (paths reach it via paths:complex_traversal). The keep_species option bears on the build stage alone, where it decides whether the PTM decorations are stripped and the content-equal results merged.

Rule	Variant	Documentation
`preparation:no_complex:deleted`		A complex with any (transitive) active descendant is deleted.
`preparation:no_complex:subunit_of_deleted_direct`		A direct subunit of a deleted complex is itself subunit-of-deleted.
`preparation:no_complex:subunit_of_deleted_transitive`		Subunit-of-deleted is transitive through nested complexes.
`preparation:no_complex:key_top_level`		A non-deleted top-level species with activity is keyed by `keptSpeciesKey(SELF)`.
`preparation:no_complex:key_promoted_subunit`		A subunit of a deleted complex with activity is promoted to top level, keyed by `promotedSubunitKey(SELF)`.
`preparation:no_complex:celldesigner:carrier`	CellDesigner	Each species is its own activity carrier.
`preparation:no_complex:sbgn_pd:carrier_entity_pool`	SBGN PD	SBGN-PD: each entity pool is its own activity carrier.
`preparation:no_complex:sbgn_pd:carrier_phenotype`	SBGN PD	SBGN-PD: each phenotype process is its own activity carrier.
`preparation:no_complex:sbgn_pd:carrier_subunit`	SBGN PD	SBGN-PD: each subunit is its own activity carrier, so a promoted subunit can be an influence endpoint (paths reach it via `paths:complex_traversal`).

`paths`

`paths:core`

Builds the direct (single-hop) kinded propagatesInfluence(SOURCE_SPECIES, TARGET_SPECIES, INFLUENCE_KIND) relation from PD reactions and modulation arcs, plus the production-cycle relations that gate transitive extension. INFLUENCE_KIND is one of positive, negative, triggering, modulation and their unknown_* twins. Reaction modifiers and the matching species→species modulation arcs map to the same kind (e.g. a trigger modifier and a triggering arc both give triggering; catalysis and physical stimulation both give positive; inhibition gives negative). Each variant defines the single reactant->product hop isDirectlyTransformedTo/2, the shared isTransformedTo/2 is its transitive closure, and isCyclicallyTransformedTo/2 marks the hops that lie inside a cycle so transitivity never propagates influence back around a production loop. The multi-hop reactant-chained transitivity itself is the excludable paths:chaining group.

Rule	Variant	Documentation
`paths:core:is_transformed_to`		Transitive closure of the single-hop `isDirectlyTransformedTo/2`: `isTransformedTo(UPSTREAM, DOWNSTREAM)` holds when DOWNSTREAM is reachable from UPSTREAM through one or more reactant->product hops (the direct hop included, as the base case). Language-agnostic; `isDirectlyTransformedTo/2` is supplied per language variant. Depends only on `isDirectlyTransformedTo`, never on `propagatesInfluence`, so the negation that gates transitivity stays stratified.
`paths:core:is_cyclically_transformed_to`		UPSTREAM and DOWNSTREAM are mutually reachable through the production graph -- both lie on a common cycle. At every transitivity guard site the hop in question is already a direct reactant->product edge, so requiring mutual reachability there is exactly equivalent to 'this hop is on a cycle'. The transitivity rules forbid extending a path across such a hop, blocking influence from leaking around production loops.
`paths:core:composes_to`		`composesTo(INCOMING_INFLUENCE_KIND, OUTGOING_INFLUENCE_KIND)`: how an influence kind transforms when a path is extended by one reactant→product hop (a reaction in CellDesigner, a process in SBGN-PD). Identity for every kind except `triggering` (a necessary-stimulation relationship is a property of the direct edge; composed through a reaction it weakens to a plain `positive` influence) and its unknown twin `unknown_triggering` → `unknown_positive`. Modulation composes like the signed kinds (stays `modulation`).
`paths:core:celldesigner:catalyzer_to_product`	CellDesigner	If a species is referred to by a catalyzer of a reaction and another species is referred to by a product of that reaction, then there is a positive path from the first to the second.
`paths:core:celldesigner:physical_stimulator_to_product`	CellDesigner	If a species is referred to by a physical stimulator of a reaction and another species is referred to by a product of that reaction, then there is a positive path from the first to the second.
`paths:core:celldesigner:trigger_to_product`	CellDesigner	If a species is referred to by a trigger of a reaction and another species is referred to by a product of that reaction, then there is a triggering path from the first to the second (a trigger→product edge is direct, so it keeps the `triggering` kind).
`paths:core:celldesigner:modulation_arc_influence`	CellDesigner	A modulation arc influences its target with the arc's kind (`hasInfluenceKind`, from the `influences:kind` group). This covers every arc type -- catalysis/physical stimulation/positive influence give `positive`, triggering gives `triggering`, inhibition/negative influence give `negative`, a bare modulation gives `modulation`, and the `unknown` twins give the `unknown_` kinds. The reaction modifier->product rules and the transitive/cycle rules remain separate.
`paths:core:celldesigner:inhibitor_to_product`	CellDesigner	If a species is referred to by an inhibitor of a reaction and another species is referred to by a product of that reaction, then there is a negative path from the first to the second.
`paths:core:celldesigner:modulator_to_product`	CellDesigner	If a species is referred to by a bare modulator of a reaction (a generic MODULATION modifier — not a physical stimulator, inhibitor or trigger; catalyzers are physical stimulators) and another species is referred to by a product of that reaction, then there is a modulation path from the first to the second.
`paths:core:celldesigner:unknown_catalyzer_to_product`	CellDesigner	If a species is referred to by an unknown catalyzer of a reaction and another species is referred to by a product of that reaction, then there is an unknown-positive path from the first to the second.
`paths:core:celldesigner:unknown_inhibitor_to_product`	CellDesigner	If a species is referred to by an unknown inhibitor of a reaction and another species is referred to by a product of that reaction, then there is an unknown-negative path from the first to the second.
`paths:core:celldesigner:is_directly_transformed_to`	CellDesigner	The single reactant->product hop in the production graph: the upstream species is referred to by a reactant and the downstream species by a product of the same reaction. Passive voice (the reaction does the transforming, not the species) keeps it language-neutral. Feeds the shared `isTransformedTo`/`isCyclicallyTransformedTo` cycle relations that gate transitive path extension; carries no influence kind itself.
`paths:core:sbgn_pd:modulation_to_product`	SBGN PD	A modulation arc's entity-pool source influences each product of its target process, carrying the arc's kind.
`paths:core:sbgn_pd:modulation_to_phenotype`	SBGN PD	A modulation arc whose target is a phenotype influences the phenotype itself (a phenotype process has no products; it is the activity).
`paths:core:sbgn_pd:is_directly_transformed_to`	SBGN PD	The single reactant->product hop in the production graph: the upstream entity pool is an element of a reactant and the downstream pool an element of a product of the same process. Passive voice (the process does the transforming, not the pool) keeps it language-neutral. Feeds the shared `isTransformedTo`/`isCyclicallyTransformedTo` cycle relations that gate transitive path extension; carries no influence kind itself.

`paths:chaining`

Excludable multi-hop transitivity: extends a propagatesInfluence path through one more reactant->product hop (a reaction in CellDesigner, a process in SBGN-PD), carrying the kind via composesTo (triggering degrades to positivelyInfluences) and refusing to extend across a hop inside a production cycle (not isCyclicallyTransformedTo). Exclude with --exclude-group paths:chaining to keep only direct single-hop influences. Depends on paths:core, which supplies both composesTo and the cycle relations.

Rule	Variant	Documentation
`paths:chaining:celldesigner:transitive_through_reaction`	CellDesigner	If there is a path from a species to an intermediate species, and the intermediate species is referred to by a reactant of a reaction whose product refers to another species, then there is a path from the first species to the second. The kind is carried through `composesTo`, which degrades `triggering`→`positive` (and `unknown_triggering`→`unknown_positive`) at the reaction hop while leaving every other kind unchanged. Extension is suppressed across a reactant->product hop that lies inside a cycle (`isCyclicallyTransformedTo`), so a source feeding a production cycle does not leak influence back around the loop onto members it directly depletes.
`paths:chaining:sbgn_pd:transitive_through_process`	SBGN PD	Extends a path through a process reactant->product hop, carrying the kind via `composesTo` (triggering degrades to positivelyInfluences). Extension is suppressed across a reactant->product hop that lies inside a cycle (`isCyclicallyTransformedTo`), so a source feeding a production cycle does not leak influence back around the loop onto members it directly depletes.

`paths:complex_traversal`

Extends paths through complex containment for the no-complex mode: a path touching a complex is propagated to/from each of its subunits so influences reach the surviving subunit activities.

Rule	Variant	Documentation
`paths:complex_traversal:into_subunits`		If an influence of a given kind propagates from a source to a complex, then it also propagates from the source to each subunit of the complex.
`paths:complex_traversal:from_subunits`		If an influence of a given kind propagates from a complex to a target, then it also propagates from each subunit of the complex to the target.

`entity`

`entity:identity`

When two elements are the same entity in different states: isSameEntityAs(ELEMENT, OTHER_ELEMENT) holds for two species sharing a template (protein, gene, RNA reference), and for two template-free elements of the same kind and name (CellDesigner) or label (SBGN-PD). State, multimer cardinality and compartment are ignored, so a species and a modified form of it are the same entity. influences:consumption uses it to tell a reaction that hands its reactant back from one that uses it up, and influences:binding_activation to tell whether the entity leaving a reaction is the one that entered it.

Rule	Variant	Documentation
`entity:identity:celldesigner:from_template`	CellDesigner	CellDesigner: two species sharing a template (protein, gene, RNA reference) are the same entity.
`entity:identity:celldesigner:kind`	CellDesigner	CellDesigner: the kind of each species class that carries no template.
`entity:identity:celldesigner:from_name`	CellDesigner	CellDesigner: two template-free species of the same kind and name are the same entity.
`entity:identity:sbgn_pd:kind`	SBGN PD	SBGN-PD: the kind shared by an entity pool, its multimer, its subunit and its multimer subunit classes, so a `macromolecule` pool and a `macromoleculeSubunit` compare as the same kind.
`entity:identity:sbgn_pd:from_label`	SBGN PD	SBGN-PD: two elements of the same kind and label are the same entity.

`influences`

`influences:kind`

Maps each modulation arc to its influence kind via hasInfluenceKind(MODULATION, INFLUENCE_KIND), the single place the arc-type->kind knowledge lives. Every group that emits a modulation-arc influence reads this relation rather than re-encoding the mapping. The mapping is per-language: CellDesigner arcs carry the sign in the arc type (catalysis, inhibition, ...), while an SBGN-PD arc's kind comes from its stimulation/inhibition/necessary-stimulation classification.

Rule	Variant	Documentation
`influences:kind:celldesigner:catalysis`	CellDesigner	A catalysis arc contributes a `positive` kind.
`influences:kind:celldesigner:physical_stimulation`	CellDesigner	A physical stimulation arc contributes a `positive` kind.
`influences:kind:celldesigner:positive_influence`	CellDesigner	A positive influence arc contributes a `positive` kind.
`influences:kind:celldesigner:triggering`	CellDesigner	A triggering arc contributes a `triggering` kind (kept on the direct edge; it degrades to `positive` when composed through a reaction).
`influences:kind:celldesigner:inhibition`	CellDesigner	An inhibition arc contributes a `negative` kind.
`influences:kind:celldesigner:negative_influence`	CellDesigner	A negative influence arc contributes a `negative` kind.
`influences:kind:celldesigner:modulation`	CellDesigner	A bare modulation arc (the generic MODULATION arc, not one of the signed/typed subtypes) contributes an unknown-sign `modulation` kind. The negations exclude the subtypes, which `modulation` is the umbrella over.
`influences:kind:celldesigner:unknown_catalysis`	CellDesigner	An unknown catalysis arc contributes an `unknown_positive` kind.
`influences:kind:celldesigner:unknown_physical_stimulation`	CellDesigner	An unknown physical stimulation arc contributes an `unknown_positive` kind.
`influences:kind:celldesigner:unknown_positive_influence`	CellDesigner	An unknown positive influence arc contributes an `unknown_positive` kind.
`influences:kind:celldesigner:unknown_triggering`	CellDesigner	An unknown triggering arc contributes an `unknown_triggering` kind (kept on the direct edge; it degrades to `unknown_positive` when composed through a reaction).
`influences:kind:celldesigner:unknown_inhibition`	CellDesigner	An unknown inhibition arc contributes an `unknown_negative` kind.
`influences:kind:celldesigner:unknown_negative_influence`	CellDesigner	An unknown negative influence arc contributes an `unknown_negative` kind.
`influences:kind:celldesigner:unknown_modulation`	CellDesigner	A bare unknown modulation arc (not one of the unknown subtypes) contributes an `unknown_modulation` kind. The negations exclude the subtypes, which `unknownModulation` is the umbrella over.
`influences:kind:sbgn_pd:necessary_stimulation`	SBGN PD	An SBGN-PD necessary stimulation contributes a `triggering` kind.
`influences:kind:sbgn_pd:stimulation`	SBGN PD	A stimulation (catalysis included) that is not a necessary stimulation contributes a `positive` kind.
`influences:kind:sbgn_pd:inhibition`	SBGN PD	An SBGN-PD inhibition contributes a `negative` kind.
`influences:kind:sbgn_pd:modulation`	SBGN PD	A bare modulation (neither stimulation nor inhibition) contributes an unknown-sign `modulation` kind.

`influences:core`

Derivation: emits new(activity(KEY)) for every activity key, and lifts every kinded path into the internal influences(SOURCE_KEY, TARGET_KEY, INFLUENCE_KIND) relation by resolving both endpoints through their activity carrier and key. Both rules are mode- and language-agnostic; the consumption/sparing reasoning lives in the separate influences:consumption group. The internal influences/3 relation is fanned out to the typed new(...) heads by the shared influences:output group.

Rule	Variant	Documentation
`influences:core:activity`		Every species with an activity key emits an activity node with that key.
`influences:core:path`		A propagated influence of any kind between two raw nodes yields an influence of that same kind between their activity-key images (via their carriers).

`influences:consumption`

Excludable consumption/sparing reasoning: a reaction depletes its reactants, so a modifier that drives the reaction also acts on every reactant that is itself an activity -- catalyzer/physicalStimulator/trigger negatively influence each consumed reactant, inhibitor positively influences each spared reactant, and the unknown modifiers contribute the unknown twins. The SBGN-PD variant walks a modulation arc onto a process the same way: a stimulation (catalysis and necessary stimulation included) negatively influences each reactant activity, an inhibition positively influences each one, a bare modulation neither. A reactant the reaction hands back as the same activity is not depleted and draws no edge; returnsReactantAsActivity carries that condition, and excluding that one rule restores the unconditional behavior. This is inference beyond what the map draws, so it is a group of its own: exclude with --exclude-group influences:consumption to keep only the influences the map states. The keep-reactions mode omits it, since that mode renders each reaction directly instead of reasoning about it.

Rule	Variant	Documentation
`influences:consumption:returns_reactant_as_activity`		A reaction hands a reactant back when one of its products is the same entity (`entity:identity`) and is itself an activity: a phosphorylation whose two forms are both activities, or a reaction listing the same species on both sides. Such a reactant is not depleted, so the consumption and sparing rules require that this does not hold. A product that is the same entity but not an activity is an inactivation and keeps its edge, as does a product that is a different entity, or the same entity sitting as a subunit of a product complex. PROCESS binds a CellDesigner reaction or an SBGN-PD process. Excluding this one rule with `--exclude-rule influences:consumption:returns_reactant_as_activity` leaves the relation underived, so the consumption rules fire unconditionally again -- useful to surface curation mistakes, which show up as an activity influenced both positively and negatively by the same source.
`influences:consumption:celldesigner:catalyzer_consumes_reactant`	CellDesigner	A catalyzer of a reaction negatively influences each reactant that is itself an activity and that the reaction does not hand back as the same activity (consumption depletes the reactant — a negative influence alongside the modifier's positive role on a product that is a different activity).
`influences:consumption:celldesigner:physical_stimulator_consumes_reactant`	CellDesigner	A physical stimulator of a reaction negatively influences each reactant that is itself an activity and that the reaction does not hand back as the same activity (consumption).
`influences:consumption:celldesigner:trigger_consumes_reactant`	CellDesigner	A trigger of a reaction negatively influences each reactant that is itself an activity and that the reaction does not hand back as the same activity (consumption is depletion, hence negative — not triggers, which is only the trigger→product relationship).
`influences:consumption:celldesigner:inhibitor_spares_reactant`	CellDesigner	An inhibitor of a reaction positively influences each reactant that is itself an activity and that the reaction does not hand back as the same activity (sparing).
`influences:consumption:celldesigner:unknown_catalyzer_consumes_reactant`	CellDesigner	An unknown catalyzer of a reaction unknown-negatively influences each reactant that is itself an activity and that the reaction does not hand back as the same activity (consumption, uncertain).
`influences:consumption:celldesigner:unknown_inhibitor_spares_reactant`	CellDesigner	An unknown inhibitor of a reaction unknown-positively influences each reactant that is itself an activity and that the reaction does not hand back as the same activity (sparing, uncertain).
`influences:consumption:sbgn_pd:stimulation_consumes_reactant`	SBGN PD	A stimulation (catalysis and necessary stimulation included -- the ontology derives both from `stimulation`) onto a process negatively influences each reactant of that process that is itself an activity and that the process does not hand back as the same activity: running the process consumes it.
`influences:consumption:sbgn_pd:inhibition_spares_reactant`	SBGN PD	An inhibition onto a process positively influences each reactant of that process that is itself an activity and that the process does not hand back as the same activity: blocking the process spares it.

`influences:binding_activation`

Excludable activation-by-binding reasoning: when a reaction turns an entity drawn inactive as a reactant (or inside a reactant complex) into an active subunit of a product complex, the binding activated it, so every other reactant of that reaction -- one that is neither the same entity nor itself activated by the same reaction -- becomes an activity (reason isBindingActivator) and positively influences the activity carrying the active subunit: its top-level complex in normal, the promoted subunit in no-complex. Two entities activated by the same reaction draw no edge between each other. Same-entity comes from the entity:identity group. The edge is direct (influences/3), so it does not chain through later reactions. Exclude with --exclude-group influences:binding_activation.

Rule	Variant	Documentation
`influences:binding_activation:is_descendant_subunit_of`		A subunit at any depth of a complex.
`influences:binding_activation:is_self_or_descendant_subunit_of`		A reaction participant itself, or a subunit of it at any depth: the forms an entity can take on one side of a reaction.
`influences:binding_activation:active_marker_from_override`		An element pinned active by `--set-active` counts as explicitly marked active.
`influences:binding_activation:activates_by_binding`		A reaction activates an entity by binding when a form of it enters the reaction without an explicit active marker (as a reactant, or inside a reactant complex) and leaves it as an explicitly active subunit of a product complex.
`influences:binding_activation:contains_inactive_reactant_of`		A reactant that is, or contains, an entity the reaction activates by binding.
`influences:binding_activation:is_binding_activator_of`		Every other reactant of the activating reaction is a binding activator of the active subunit: one that is neither the same entity as the subunit nor itself activated by the reaction. Requiring the subunit's activity key keeps a suppressed subunit (`--set-inactive`) from making its partners activities.
`influences:binding_activation:candidate`		A binding activator is an activity candidate (reason `isBindingActivator`); it still passes through the `activity:core` bridge, so the vetoes apply.
`influences:binding_activation:influence`		A binding activator positively influences the activity carrying the active subunit. The source is the activator's own key, or -- when the activator is a complex dissolved in `no-complex` -- the key of each of its promoted subunits.
`influences:binding_activation:celldesigner:active_marker_from_active_flag`	CellDesigner	CellDesigner: a species whose `hasActive` flag is 1 is explicitly marked active.
`influences:binding_activation:celldesigner:active_marker_from_structural_state`	CellDesigner	CellDesigner: a species in an "active" structural state is explicitly marked active.
`influences:binding_activation:sbgn_pd:active_marker_from_state_variable`	SBGN PD	SBGN-PD: an entity pool or subunit carrying an "active" state variable is explicitly marked active.

`influences:output`

Shared fan-out from the internal influences(SOURCE, TARGET, INFLUENCE_KIND) relation to the typed new(...) influence heads — one rule per kind. Every pipeline converges on influences/3; this group is the single place that turns a kind into its output predicate.

Rule	Variant	Documentation
`influences:output:positive`		A `positive` influence emits a `positivelyInfluences` edge (PositiveInfluence).
`influences:output:negative`		A `negative` influence emits a `negativelyInfluences` edge (NegativeInfluence).
`influences:output:modulation`		A `modulation` influence emits a `modulates` edge (Modulation).
`influences:output:triggering`		A `triggering` influence emits a `triggers` edge (Triggering).
`influences:output:unknown_positive`		An `unknown_positive` influence emits an `unknownPositivelyInfluences` edge (UnknownPositiveInfluence).
`influences:output:unknown_negative`		An `unknown_negative` influence emits an `unknownNegativelyInfluences` edge (UnknownNegativeInfluence).
`influences:output:unknown_modulation`		An `unknown_modulation` influence emits an `unknownModulates` edge (UnknownModulation).
`influences:output:unknown_triggering`		An `unknown_triggering` influence emits an `unknownTriggers` edge (UnknownTriggering).

`gates`

`gates:core`

Authored logical operators (CellDesigner BooleanLogicGate, SBGN-PD LogicalOperator): emits the operator node (logicalOperator/2, token-typed), its input edges (logicalOperatorInput/2, each input resolved through carrier/key -- or, for SBGN-PD, through the referred operator's own key when the input refers to another logical operator), and the operator-sourced influence written straight into the internal influences/3 relation by reusing the existing propagatesInfluence(OPERATOR, TARGET, INFLUENCE_KIND) closure. The node and influence rules are guarded on the input edges, so an operator with zero resolved inputs emits neither a node nor a sourced influence, and one with some resolved inputs keeps them all. The widened influence source union (predicates._INFLUENCE_SOURCE) lets influences:output fan these out with no change. Provenance-agnostic.

Rule	Variant	Documentation
`gates:core:celldesigner:node_and`	CellDesigner	An `andGate` with at least one resolved input emits an AND logical-operator node.
`gates:core:celldesigner:node_or`	CellDesigner	An `orGate` with at least one resolved input emits an OR logical-operator node.
`gates:core:celldesigner:node_not`	CellDesigner	A `notGate` with at least one resolved input emits a NOT logical-operator node. The token is `not_` because bare `not` is a reserved clingo keyword.
`gates:core:celldesigner:node_unknown`	CellDesigner	An `unknownGate` with at least one resolved input emits an unknown-type logical-operator node.
`gates:core:celldesigner:input_edge`	CellDesigner	Each gate input is resolved through its activity carrier and key (mirroring `influences:core:path`), so an input that is a subunit resolves to its top-level complex's key. The `booleanLogicGate` umbrella matches every gate type via the ontology's isa rules.
`gates:core:celldesigner:influence`	CellDesigner	One rule covering both Shape A (gate is a reaction modifier) and Shape B (gate is a modulation source): the `paths:core` rules already bind a `propagatesInfluence/3` whose source is the gate, so the gate only resolves its TARGET through carrier/key and writes the influence keyed by the operator. Inherits the transitive closure (Decision D1). The `booleanLogicGate` guard is essential -- without it every species `propagatesInfluence/3` source would be read as an operator key. The input-existence guard drops an operator with no resolved input -- it emits neither a node nor a sourced influence; an operator with some resolved inputs keeps them all.
`gates:core:sbgn_pd:node_and`	SBGN PD	An `andOperator` with at least one resolved input emits an AND logical-operator node.
`gates:core:sbgn_pd:node_or`	SBGN PD	An `orOperator` with at least one resolved input emits an OR logical-operator node.
`gates:core:sbgn_pd:node_not`	SBGN PD	A `notOperator` with at least one resolved input emits a NOT logical-operator node. The token is `not_` because bare `not` is a reserved clingo keyword. (SBGN-PD has no unknown-operator type.)
`gates:core:sbgn_pd:input_edge`	SBGN PD	SBGN-PD parallel of the CellDesigner input-edge rule, guarded on the `logicalOperator` umbrella (derived from the per-type operators via the ontology isa rules).
`gates:core:sbgn_pd:input_edge_operator`	SBGN PD	An SBGN-PD operator input whose referred element is itself a logical operator resolves through that operator's key instead of through an activity candidate. Guarded on the input operator emitting a node, so an input operator that is itself dropped contributes no edge. This rule and the node rules are mutually recursive, positively so: an operator emits a node when it has an input edge, and an operator input contributes an edge when the input operator emits a node. The least fixpoint is exactly the intended reading -- an operator survives when at least one of its inputs is an activity or is itself a surviving operator -- and a cyclic operator graph with no activity underneath it emits nothing. (CellDesigner has no parallel: a `BooleanLogicGateInput` always refers to a species, so its gates cannot nest.)
`gates:core:sbgn_pd:influence`	SBGN PD	SBGN-PD parallel of the CellDesigner operator-sourced influence rule (Shape B: the operator is a modulation source). Reuses the `propagatesInfluence(OPERATOR, TARGET, INFLUENCE_KIND)` closure emitted by `paths:core`, resolving only the target through carrier/key. The input-existence guard drops an operator with no resolved input -- it emits neither a node nor a sourced influence; an operator with some resolved inputs keeps them all.

`keep_reactions`

`keep_reactions:activity`

The keep-reactions premise that every species is an activity, replacing the structural-reason activity:* feature-groups (each of which is inert once every species is a candidate, so the mode omits them). Unlike the --set-all-active toggle this rule carries no not hasSubunit guard: a subunit is a candidate too, which does not make it an activity of its own -- preparation:complex:key keys it by the keptSpeciesKey of its outermost complex -- but it does mean a reaction, modulation arc or gate input touching a subunit routes to the containing complex instead of being dropped for want of an activity key.

Rule	Variant	Documentation
`keep_reactions:activity:from_species`		Every species is an activity candidate, for the sole reason that it is a species (reason `isSpecies`). It still passes through the `activity:core` bridge, so `--set-inactive` and `--set-all-inactive` veto candidates in this mode exactly as in any other.

`keep_reactions:influences`

The keep-reactions premise that every reaction is kept: each (reactant, product) pair of a reaction becomes one positive influence. positivelyInfluences rather than triggers -- consuming a reactant to make a product is a contribution to it, not the necessary-stimulation relationship triggers (CellDesigner Triggering, SBGN-AF NecessaryStimulation) asserts. The rule writes propagatesInfluence/3 rather than influences/3 so the shared influences:core:path bridge resolves both endpoints through their carrier and key, routing a subunit endpoint to its top-level complex. Reactant and product may resolve to the same activity (a reaction whose participants share a complex, or a state transition drawn on a single species), and the resulting self-influence is emitted like any other.

Rule	Variant	Documentation
`keep_reactions:influences:reactant_to_product`		Each reactant of a reaction positively influences each product of that reaction. This is the one rule that makes a reaction itself an influence: in the other modes the reactant->product hop only feeds the cycle relations, and a reactant is an influence source only when it activates a binding partner (`influences:binding_activation`).

Rule index

All rules in alphabetical order (identifiers are group- and variant-prefixed).

Rule	Group	Variant	Modes	Summary
`activity:active_marker:celldesigner:from_active_flag`	`activity:active_marker`	CellDesigner	`normal`, `no-complex`	A species explicitly marked as active is an activity candidate.
`activity:active_marker:celldesigner:from_active_structural_state`	`activity:active_marker`	CellDesigner	`normal`, `no-complex`	A species in an active structural state is an activity candidate.
`activity:active_marker:sbgn_pd:from_active_state_variable`	`activity:active_marker`	SBGN PD	`normal`, `no-complex`	An entity pool in an active state is an activity candidate.
`activity:active_marker:sbgn_pd:from_active_subunit_state_variable`	`activity:active_marker`	SBGN PD	`normal`, `no-complex`	A subunit in an active state is an activity candidate.
`activity:core:celldesigner:from_global_activate`	`activity:core`	CellDesigner	all	Under the set-all-active toggle, every top-level species is an activity candidate.
`activity:core:from_candidate`	`activity:core`		all	An activity candidate becomes an actual activity unless it has been vetoed.
`activity:core:from_global_suppress`	`activity:core`		all	The set-all-inactive toggle suppresses every activity candidate, except those pinned active per id.
`activity:core:sbgn_pd:from_global_activate`	`activity:core`	SBGN PD	all	Under the set-all-active toggle, every entity pool is an activity candidate.
`activity:gate_input:celldesigner:from_gate_input`	`activity:gate_input`	CellDesigner	`normal`, `no-complex`	A species feeding a boolean logic gate is an activity candidate.
`activity:gate_input:sbgn_pd:from_operator_input`	`activity:gate_input`	SBGN PD	`normal`, `no-complex`	An entity pool feeding a logical operator is an activity candidate.
`activity:modulation_source:celldesigner:from_modulation_source`	`activity:modulation_source`	CellDesigner	`normal`, `no-complex`	A species that is the source of a modulation arc is an activity candidate.
`activity:modulation_source:celldesigner:from_reaction_modulator`	`activity:modulation_source`	CellDesigner	`normal`, `no-complex`	A species that modulates a reaction is an activity candidate.
`activity:modulation_source:sbgn_pd:from_modulation_source`	`activity:modulation_source`	SBGN PD	`normal`, `no-complex`	An entity pool that is the source of a modulation arc is an activity candidate.
`activity:phenotype:from_phenotype`	`activity:phenotype`		`normal`, `no-complex`	A phenotype is always an activity candidate.
`entity:identity:celldesigner:from_name`	`entity:identity`	CellDesigner	`normal`, `no-complex`	CellDesigner: two template-free species of the same kind and name are the same entity.
`entity:identity:celldesigner:from_template`	`entity:identity`	CellDesigner	`normal`, `no-complex`	CellDesigner: two species sharing a template (protein, gene, RNA reference) are the same entity.
`entity:identity:celldesigner:kind`	`entity:identity`	CellDesigner	`normal`, `no-complex`	CellDesigner: the kind of each species class that carries no template.
`entity:identity:sbgn_pd:from_label`	`entity:identity`	SBGN PD	`normal`, `no-complex`	SBGN-PD: two elements of the same kind and label are the same entity.
`entity:identity:sbgn_pd:kind`	`entity:identity`	SBGN PD	`normal`, `no-complex`	SBGN-PD: the kind shared by an entity pool, its multimer, its subunit and its multimer subunit classes, so a `macromolecule` pool and a `macromoleculeSubunit` compare as the same kind.
`gates:core:celldesigner:influence`	`gates:core`	CellDesigner	all	One rule covering both Shape A (gate is a reaction modifier) and Shape B (gate is a modulation source): the `paths:core` rules already bind a `propagatesInfluence/3` whose source is the gate, so the gate only resolves its TARGET through carrier/key and writes the influence keyed by the operator.
`gates:core:celldesigner:input_edge`	`gates:core`	CellDesigner	all	Each gate input is resolved through its activity carrier and key (mirroring `influences:core:path`), so an input that is a subunit resolves to its top-level complex's key.
`gates:core:celldesigner:node_and`	`gates:core`	CellDesigner	all	An `andGate` with at least one resolved input emits an AND logical-operator node.
`gates:core:celldesigner:node_not`	`gates:core`	CellDesigner	all	A `notGate` with at least one resolved input emits a NOT logical-operator node.
`gates:core:celldesigner:node_or`	`gates:core`	CellDesigner	all	An `orGate` with at least one resolved input emits an OR logical-operator node.
`gates:core:celldesigner:node_unknown`	`gates:core`	CellDesigner	all	An `unknownGate` with at least one resolved input emits an unknown-type logical-operator node.
`gates:core:sbgn_pd:influence`	`gates:core`	SBGN PD	all	SBGN-PD parallel of the CellDesigner operator-sourced influence rule (Shape B: the operator is a modulation source).
`gates:core:sbgn_pd:input_edge`	`gates:core`	SBGN PD	all	SBGN-PD parallel of the CellDesigner input-edge rule, guarded on the `logicalOperator` umbrella (derived from the per-type operators via the ontology isa rules).
`gates:core:sbgn_pd:input_edge_operator`	`gates:core`	SBGN PD	all	An SBGN-PD operator input whose referred element is itself a logical operator resolves through that operator's key instead of through an activity candidate.
`gates:core:sbgn_pd:node_and`	`gates:core`	SBGN PD	all	An `andOperator` with at least one resolved input emits an AND logical-operator node.
`gates:core:sbgn_pd:node_not`	`gates:core`	SBGN PD	all	A `notOperator` with at least one resolved input emits a NOT logical-operator node.
`gates:core:sbgn_pd:node_or`	`gates:core`	SBGN PD	all	An `orOperator` with at least one resolved input emits an OR logical-operator node.
`influences:binding_activation:activates_by_binding`	`influences:binding_activation`		`normal`, `no-complex`	A reaction activates an entity by binding when a form of it enters the reaction without an explicit active marker (as a reactant, or inside a reactant complex) and leaves it as an explicitly active subunit of a product complex.
`influences:binding_activation:active_marker_from_override`	`influences:binding_activation`		`normal`, `no-complex`	An element pinned active by `--set-active` counts as explicitly marked active.
`influences:binding_activation:candidate`	`influences:binding_activation`		`normal`, `no-complex`	A binding activator is an activity candidate (reason `isBindingActivator`); it still passes through the `activity:core` bridge, so the vetoes apply.
`influences:binding_activation:celldesigner:active_marker_from_active_flag`	`influences:binding_activation`	CellDesigner	`normal`, `no-complex`	CellDesigner: a species whose `hasActive` flag is 1 is explicitly marked active.
`influences:binding_activation:celldesigner:active_marker_from_structural_state`	`influences:binding_activation`	CellDesigner	`normal`, `no-complex`	CellDesigner: a species in an "active" structural state is explicitly marked active.
`influences:binding_activation:contains_inactive_reactant_of`	`influences:binding_activation`		`normal`, `no-complex`	A reactant that is, or contains, an entity the reaction activates by binding.
`influences:binding_activation:influence`	`influences:binding_activation`		`normal`, `no-complex`	A binding activator positively influences the activity carrying the active subunit.
`influences:binding_activation:is_binding_activator_of`	`influences:binding_activation`		`normal`, `no-complex`	Every other reactant of the activating reaction is a binding activator of the active subunit: one that is neither the same entity as the subunit nor itself activated by the reaction.
`influences:binding_activation:is_descendant_subunit_of`	`influences:binding_activation`		`normal`, `no-complex`	A subunit at any depth of a complex.
`influences:binding_activation:is_self_or_descendant_subunit_of`	`influences:binding_activation`		`normal`, `no-complex`	A reaction participant itself, or a subunit of it at any depth: the forms an entity can take on one side of a reaction.
`influences:binding_activation:sbgn_pd:active_marker_from_state_variable`	`influences:binding_activation`	SBGN PD	`normal`, `no-complex`	SBGN-PD: an entity pool or subunit carrying an "active" state variable is explicitly marked active.
`influences:consumption:celldesigner:catalyzer_consumes_reactant`	`influences:consumption`	CellDesigner	`normal`, `no-complex`	A catalyzer of a reaction negatively influences each reactant that is itself an activity and that the reaction does not hand back as the same activity (consumption depletes the reactant — a negative influence alongside the modifier's positive role on a product that is a different activity).
`influences:consumption:celldesigner:inhibitor_spares_reactant`	`influences:consumption`	CellDesigner	`normal`, `no-complex`	An inhibitor of a reaction positively influences each reactant that is itself an activity and that the reaction does not hand back as the same activity (sparing).
`influences:consumption:celldesigner:physical_stimulator_consumes_reactant`	`influences:consumption`	CellDesigner	`normal`, `no-complex`	A physical stimulator of a reaction negatively influences each reactant that is itself an activity and that the reaction does not hand back as the same activity (consumption).
`influences:consumption:celldesigner:trigger_consumes_reactant`	`influences:consumption`	CellDesigner	`normal`, `no-complex`	A trigger of a reaction negatively influences each reactant that is itself an activity and that the reaction does not hand back as the same activity (consumption is depletion, hence negative — not triggers, which is only the trigger→product relationship).
`influences:consumption:celldesigner:unknown_catalyzer_consumes_reactant`	`influences:consumption`	CellDesigner	`normal`, `no-complex`	An unknown catalyzer of a reaction unknown-negatively influences each reactant that is itself an activity and that the reaction does not hand back as the same activity (consumption, uncertain).
`influences:consumption:celldesigner:unknown_inhibitor_spares_reactant`	`influences:consumption`	CellDesigner	`normal`, `no-complex`	An unknown inhibitor of a reaction unknown-positively influences each reactant that is itself an activity and that the reaction does not hand back as the same activity (sparing, uncertain).
`influences:consumption:returns_reactant_as_activity`	`influences:consumption`		`normal`, `no-complex`	A reaction hands a reactant back when one of its products is the same entity (`entity:identity`) and is itself an activity: a phosphorylation whose two forms are both activities, or a reaction listing the same species on both sides.
`influences:consumption:sbgn_pd:inhibition_spares_reactant`	`influences:consumption`	SBGN PD	`normal`, `no-complex`	An inhibition onto a process positively influences each reactant of that process that is itself an activity and that the process does not hand back as the same activity: blocking the process spares it.
`influences:consumption:sbgn_pd:stimulation_consumes_reactant`	`influences:consumption`	SBGN PD	`normal`, `no-complex`	A stimulation (catalysis and necessary stimulation included -- the ontology derives both from `stimulation`) onto a process negatively influences each reactant of that process that is itself an activity and that the process does not hand back as the same activity: running the process consumes it.
`influences:core:activity`	`influences:core`		all	Every species with an activity key emits an activity node with that key.
`influences:core:path`	`influences:core`		all	A propagated influence of any kind between two raw nodes yields an influence of that same kind between their activity-key images (via their carriers).
`influences:kind:celldesigner:catalysis`	`influences:kind`	CellDesigner	all	A catalysis arc contributes a `positive` kind.
`influences:kind:celldesigner:inhibition`	`influences:kind`	CellDesigner	all	An inhibition arc contributes a `negative` kind.
`influences:kind:celldesigner:modulation`	`influences:kind`	CellDesigner	all	A bare modulation arc (the generic MODULATION arc, not one of the signed/typed subtypes) contributes an unknown-sign `modulation` kind.
`influences:kind:celldesigner:negative_influence`	`influences:kind`	CellDesigner	all	A negative influence arc contributes a `negative` kind.
`influences:kind:celldesigner:physical_stimulation`	`influences:kind`	CellDesigner	all	A physical stimulation arc contributes a `positive` kind.
`influences:kind:celldesigner:positive_influence`	`influences:kind`	CellDesigner	all	A positive influence arc contributes a `positive` kind.
`influences:kind:celldesigner:triggering`	`influences:kind`	CellDesigner	all	A triggering arc contributes a `triggering` kind (kept on the direct edge; it degrades to `positive` when composed through a reaction).
`influences:kind:celldesigner:unknown_catalysis`	`influences:kind`	CellDesigner	all	An unknown catalysis arc contributes an `unknown_positive` kind.
`influences:kind:celldesigner:unknown_inhibition`	`influences:kind`	CellDesigner	all	An unknown inhibition arc contributes an `unknown_negative` kind.
`influences:kind:celldesigner:unknown_modulation`	`influences:kind`	CellDesigner	all	A bare unknown modulation arc (not one of the unknown subtypes) contributes an `unknown_modulation` kind.
`influences:kind:celldesigner:unknown_negative_influence`	`influences:kind`	CellDesigner	all	An unknown negative influence arc contributes an `unknown_negative` kind.
`influences:kind:celldesigner:unknown_physical_stimulation`	`influences:kind`	CellDesigner	all	An unknown physical stimulation arc contributes an `unknown_positive` kind.
`influences:kind:celldesigner:unknown_positive_influence`	`influences:kind`	CellDesigner	all	An unknown positive influence arc contributes an `unknown_positive` kind.
`influences:kind:celldesigner:unknown_triggering`	`influences:kind`	CellDesigner	all	An unknown triggering arc contributes an `unknown_triggering` kind (kept on the direct edge; it degrades to `unknown_positive` when composed through a reaction).
`influences:kind:sbgn_pd:inhibition`	`influences:kind`	SBGN PD	all	An SBGN-PD inhibition contributes a `negative` kind.
`influences:kind:sbgn_pd:modulation`	`influences:kind`	SBGN PD	all	A bare modulation (neither stimulation nor inhibition) contributes an unknown-sign `modulation` kind.
`influences:kind:sbgn_pd:necessary_stimulation`	`influences:kind`	SBGN PD	all	An SBGN-PD necessary stimulation contributes a `triggering` kind.
`influences:kind:sbgn_pd:stimulation`	`influences:kind`	SBGN PD	all	A stimulation (catalysis included) that is not a necessary stimulation contributes a `positive` kind.
`influences:output:modulation`	`influences:output`		all	A `modulation` influence emits a `modulates` edge (Modulation).
`influences:output:negative`	`influences:output`		all	A `negative` influence emits a `negativelyInfluences` edge (NegativeInfluence).
`influences:output:positive`	`influences:output`		all	A `positive` influence emits a `positivelyInfluences` edge (PositiveInfluence).
`influences:output:triggering`	`influences:output`		all	A `triggering` influence emits a `triggers` edge (Triggering).
`influences:output:unknown_modulation`	`influences:output`		all	An `unknown_modulation` influence emits an `unknownModulates` edge (UnknownModulation).
`influences:output:unknown_negative`	`influences:output`		all	An `unknown_negative` influence emits an `unknownNegativelyInfluences` edge (UnknownNegativeInfluence).
`influences:output:unknown_positive`	`influences:output`		all	An `unknown_positive` influence emits an `unknownPositivelyInfluences` edge (UnknownPositiveInfluence).
`influences:output:unknown_triggering`	`influences:output`		all	An `unknown_triggering` influence emits an `unknownTriggers` edge (UnknownTriggering).
`keep_reactions:activity:from_species`	`keep_reactions:activity`		`keep-reactions`	Every species is an activity candidate, for the sole reason that it is a species (reason `isSpecies`).
`keep_reactions:influences:reactant_to_product`	`keep_reactions:influences`		`keep-reactions`	Each reactant of a reaction positively influences each product of that reaction.
`paths:chaining:celldesigner:transitive_through_reaction`	`paths:chaining`	CellDesigner	`normal`, `no-complex`	If there is a path from a species to an intermediate species, and the intermediate species is referred to by a reactant of a reaction whose product refers to another species, then there is a path from the first species to the second.
`paths:chaining:sbgn_pd:transitive_through_process`	`paths:chaining`	SBGN PD	`normal`, `no-complex`	Extends a path through a process reactant->product hop, carrying the kind via `composesTo` (triggering degrades to positivelyInfluences).
`paths:complex_traversal:from_subunits`	`paths:complex_traversal`		`no-complex`	If an influence of a given kind propagates from a complex to a target, then it also propagates from each subunit of the complex to the target.
`paths:complex_traversal:into_subunits`	`paths:complex_traversal`		`no-complex`	If an influence of a given kind propagates from a source to a complex, then it also propagates from the source to each subunit of the complex.
`paths:core:celldesigner:catalyzer_to_product`	`paths:core`	CellDesigner	all	If a species is referred to by a catalyzer of a reaction and another species is referred to by a product of that reaction, then there is a positive path from the first to the second.
`paths:core:celldesigner:inhibitor_to_product`	`paths:core`	CellDesigner	all	If a species is referred to by an inhibitor of a reaction and another species is referred to by a product of that reaction, then there is a negative path from the first to the second.
`paths:core:celldesigner:is_directly_transformed_to`	`paths:core`	CellDesigner	all	The single reactant->product hop in the production graph: the upstream species is referred to by a reactant and the downstream species by a product of the same reaction.
`paths:core:celldesigner:modulation_arc_influence`	`paths:core`	CellDesigner	all	A modulation arc influences its target with the arc's kind (`hasInfluenceKind`, from the `influences:kind` group).
`paths:core:celldesigner:modulator_to_product`	`paths:core`	CellDesigner	all	If a species is referred to by a bare modulator of a reaction (a generic MODULATION modifier — not a physical stimulator, inhibitor or trigger; catalyzers are physical stimulators) and another species is referred to by a product of that reaction, then there is a modulation path from the first to the second.
`paths:core:celldesigner:physical_stimulator_to_product`	`paths:core`	CellDesigner	all	If a species is referred to by a physical stimulator of a reaction and another species is referred to by a product of that reaction, then there is a positive path from the first to the second.
`paths:core:celldesigner:trigger_to_product`	`paths:core`	CellDesigner	all	If a species is referred to by a trigger of a reaction and another species is referred to by a product of that reaction, then there is a triggering path from the first to the second (a trigger→product edge is direct, so it keeps the `triggering` kind).
`paths:core:celldesigner:unknown_catalyzer_to_product`	`paths:core`	CellDesigner	all	If a species is referred to by an unknown catalyzer of a reaction and another species is referred to by a product of that reaction, then there is an unknown-positive path from the first to the second.
`paths:core:celldesigner:unknown_inhibitor_to_product`	`paths:core`	CellDesigner	all	If a species is referred to by an unknown inhibitor of a reaction and another species is referred to by a product of that reaction, then there is an unknown-negative path from the first to the second.
`paths:core:composes_to`	`paths:core`		all	`composesTo(INCOMING_INFLUENCE_KIND, OUTGOING_INFLUENCE_KIND)`: how an influence kind transforms when a path is extended by one reactant→product hop (a reaction in CellDesigner, a process in SBGN-PD).
`paths:core:is_cyclically_transformed_to`	`paths:core`		all	UPSTREAM and DOWNSTREAM are mutually reachable through the production graph -- both lie on a common cycle.
`paths:core:is_transformed_to`	`paths:core`		all	Transitive closure of the single-hop `isDirectlyTransformedTo/2`: `isTransformedTo(UPSTREAM, DOWNSTREAM)` holds when DOWNSTREAM is reachable from UPSTREAM through one or more reactant->product hops (the direct hop included, as the base case).
`paths:core:sbgn_pd:is_directly_transformed_to`	`paths:core`	SBGN PD	all	The single reactant->product hop in the production graph: the upstream entity pool is an element of a reactant and the downstream pool an element of a product of the same process.
`paths:core:sbgn_pd:modulation_to_phenotype`	`paths:core`	SBGN PD	all	A modulation arc whose target is a phenotype influences the phenotype itself (a phenotype process has no products; it is the activity).
`paths:core:sbgn_pd:modulation_to_product`	`paths:core`	SBGN PD	all	A modulation arc's entity-pool source influences each product of its target process, carrying the arc's kind.
`preparation:complex:celldesigner:carrier`	`preparation:complex`	CellDesigner	`normal`, `keep-reactions`	Each species is its own activity carrier (no rerouting; a subunit endpoint is rerouted to its top-level complex by the `topology:top_level` key, not by the carrier).
`preparation:complex:key`	`preparation:complex`		`normal`, `keep-reactions`	A species with activity is keyed by the `keptSpeciesKey` of its top-level entity (itself when top-level; its outermost complex when a subunit).
`preparation:complex:sbgn_pd:carrier_entity_pool`	`preparation:complex`	SBGN PD	`normal`, `keep-reactions`	SBGN-PD: each entity pool is its own activity carrier.
`preparation:complex:sbgn_pd:carrier_phenotype`	`preparation:complex`	SBGN PD	`normal`, `keep-reactions`	SBGN-PD: each phenotype process is its own activity carrier (phenotypes are activities, not entity pools).
`preparation:no_complex:celldesigner:carrier`	`preparation:no_complex`	CellDesigner	`no-complex`	Each species is its own activity carrier.
`preparation:no_complex:deleted`	`preparation:no_complex`		`no-complex`	A complex with any (transitive) active descendant is deleted.
`preparation:no_complex:key_promoted_subunit`	`preparation:no_complex`		`no-complex`	A subunit of a deleted complex with activity is promoted to top level, keyed by `promotedSubunitKey(SELF)`.
`preparation:no_complex:key_top_level`	`preparation:no_complex`		`no-complex`	A non-deleted top-level species with activity is keyed by `keptSpeciesKey(SELF)`.
`preparation:no_complex:sbgn_pd:carrier_entity_pool`	`preparation:no_complex`	SBGN PD	`no-complex`	SBGN-PD: each entity pool is its own activity carrier.
`preparation:no_complex:sbgn_pd:carrier_phenotype`	`preparation:no_complex`	SBGN PD	`no-complex`	SBGN-PD: each phenotype process is its own activity carrier.
`preparation:no_complex:sbgn_pd:carrier_subunit`	`preparation:no_complex`	SBGN PD	`no-complex`	SBGN-PD: each subunit is its own activity carrier, so a promoted subunit can be an influence endpoint (paths reach it via `paths:complex_traversal`).
`preparation:no_complex:subunit_of_deleted_direct`	`preparation:no_complex`		`no-complex`	A direct subunit of a deleted complex is itself subunit-of-deleted.
`preparation:no_complex:subunit_of_deleted_transitive`	`preparation:no_complex`		`no-complex`	Subunit-of-deleted is transitive through nested complexes.
`topology:core:has_active_descendant_direct`	`topology:core`		all	A complex has an active descendant if any direct subunit has activity.
`topology:core:has_active_descendant_transitive`	`topology:core`		all	The `hasActiveDescendantSubunit` relation is transitive through complex containment.
`topology:core:is_subunit`	`topology:core`		all	A species is a subunit if it appears on the right side of any `hasSubunit` relation.
`topology:top_level:celldesigner:self`	`topology:top_level`	CellDesigner	`normal`, `keep-reactions`	CellDesigner: a species that is not a subunit of any complex is its own top-level entity.
`topology:top_level:recursive`	`topology:top_level`		`normal`, `keep-reactions`	A subunit resolves to the same top-level entity as its parent complex, recursively through nested complexes -- so a subunit at any depth resolves to its outermost complex.
`topology:top_level:sbgn_pd:phenotype_self`	`topology:top_level`	SBGN PD	`normal`, `keep-reactions`	SBGN-PD: a phenotype is a process, not an entity pool, so the entity-pool self-rule never keys it; a phenotype is never a subunit, so it is always its own top-level entity.
`topology:top_level:sbgn_pd:self`	`topology:top_level`	SBGN PD	`normal`, `keep-reactions`	SBGN-PD: an entity pool that is not a subunit of any complex is its own top-level entity.