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+ + + + + + + + + + + +An individual activity in a causal model, representing the individual molecular activity of a single gene product or complex in the context of a particular model
+URI: gocam:Activity
+Name | +Cardinality and Range | +Description | +Inheritance | +
---|---|---|---|
id | +1 Uriorcurie |
+Identifier of the activity unit | +direct | +
enabled_by | +0..1 EnabledByAssociation |
+The gene product or complex that carries out the activity | +direct | +
molecular_function | +0..1 MolecularFunctionAssociation |
+The molecular function that is carried out by the gene product or complex | +direct | +
occurs_in | +0..1 CellularAnatomicalEntityAssociation |
+The cellular location in which the activity occurs | +direct | +
part_of | +0..1 BiologicalProcessAssociation |
+The larger biological process in which the activity is a part | +direct | +
has_direct_input | +0..1 MoleculeAssociation |
+The input molecules that are directly consumed by the activity | +direct | +
has_direct_output | +0..1 MoleculeAssociation |
+The output molecules that are directly produced by the activity | +direct | +
causal_associations | +* CausalAssociation |
+The causal associations that connect this activity to other activities | +direct | +
provenances | +* ProvenanceInfo |
+Provenance information for the activity | +direct | +
used by | +used in | +type | +used | +
---|---|---|---|
Model | +activities | +range | +Activity | +
CausalAssociation | +downstream_activity | +range | +Activity | +
Mapping Type | +Mapped Value | +
---|---|
self | +gocam:Activity | +
native | +gocam:Activity | +
name: Activity
+description: An individual activity in a causal model, representing the individual
+ molecular activity of a single gene product or complex in the context of a particular
+ model
+from_schema: https://w3id.org/gocam
+aliases:
+- annoton
+attributes:
+ id:
+ name: id
+ description: Identifier of the activity unit. Should be in gocam namespace.
+ comments:
+ - Typically does not need to be exposed to end-user, this exists to allow activity
+ flows
+ from_schema: https://w3id.org/gocam
+ identifier: true
+ domain_of:
+ - Model
+ - Activity
+ - Object
+ range: uriorcurie
+ required: true
+ enabled_by:
+ name: enabled_by
+ description: The gene product or complex that carries out the activity
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ domain_of:
+ - Activity
+ range: EnabledByAssociation
+ inlined: true
+ molecular_function:
+ name: molecular_function
+ description: The molecular function that is carried out by the gene product or
+ complex
+ todos:
+ - currently BP, CC etc are at the level of the activity, not the MolecularFunctionAssociation
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ domain_of:
+ - Activity
+ range: MolecularFunctionAssociation
+ inlined: true
+ occurs_in:
+ name: occurs_in
+ description: The cellular location in which the activity occurs
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ domain_of:
+ - Activity
+ range: CellularAnatomicalEntityAssociation
+ inlined: true
+ part_of:
+ name: part_of
+ description: The larger biological process in which the activity is a part
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ domain_of:
+ - Activity
+ range: BiologicalProcessAssociation
+ inlined: true
+ has_direct_input:
+ name: has_direct_input
+ description: The input molecules that are directly consumed by the activity
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ domain_of:
+ - Activity
+ range: MoleculeAssociation
+ inlined: true
+ has_direct_output:
+ name: has_direct_output
+ description: The output molecules that are directly produced by the activity
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ domain_of:
+ - Activity
+ range: MoleculeAssociation
+ inlined: true
+ causal_associations:
+ name: causal_associations
+ description: The causal associations that connect this activity to other activities
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ multivalued: true
+ domain_of:
+ - Activity
+ range: CausalAssociation
+ inlined: true
+ inlined_as_list: true
+ provenances:
+ name: provenances
+ description: Provenance information for the activity
+ from_schema: https://w3id.org/gocam
+ multivalued: true
+ domain_of:
+ - Model
+ - Activity
+ - EvidenceItem
+ - Association
+ range: ProvenanceInfo
+ inlined: true
+ inlined_as_list: true
+
+
+name: Activity
+description: An individual activity in a causal model, representing the individual
+ molecular activity of a single gene product or complex in the context of a particular
+ model
+from_schema: https://w3id.org/gocam
+aliases:
+- annoton
+attributes:
+ id:
+ name: id
+ description: Identifier of the activity unit. Should be in gocam namespace.
+ comments:
+ - Typically does not need to be exposed to end-user, this exists to allow activity
+ flows
+ from_schema: https://w3id.org/gocam
+ identifier: true
+ alias: id
+ owner: Activity
+ domain_of:
+ - Model
+ - Activity
+ - Object
+ range: uriorcurie
+ required: true
+ enabled_by:
+ name: enabled_by
+ description: The gene product or complex that carries out the activity
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ alias: enabled_by
+ owner: Activity
+ domain_of:
+ - Activity
+ range: EnabledByAssociation
+ inlined: true
+ molecular_function:
+ name: molecular_function
+ description: The molecular function that is carried out by the gene product or
+ complex
+ todos:
+ - currently BP, CC etc are at the level of the activity, not the MolecularFunctionAssociation
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ alias: molecular_function
+ owner: Activity
+ domain_of:
+ - Activity
+ range: MolecularFunctionAssociation
+ inlined: true
+ occurs_in:
+ name: occurs_in
+ description: The cellular location in which the activity occurs
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ alias: occurs_in
+ owner: Activity
+ domain_of:
+ - Activity
+ range: CellularAnatomicalEntityAssociation
+ inlined: true
+ part_of:
+ name: part_of
+ description: The larger biological process in which the activity is a part
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ alias: part_of
+ owner: Activity
+ domain_of:
+ - Activity
+ range: BiologicalProcessAssociation
+ inlined: true
+ has_direct_input:
+ name: has_direct_input
+ description: The input molecules that are directly consumed by the activity
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ alias: has_direct_input
+ owner: Activity
+ domain_of:
+ - Activity
+ range: MoleculeAssociation
+ inlined: true
+ has_direct_output:
+ name: has_direct_output
+ description: The output molecules that are directly produced by the activity
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ alias: has_direct_output
+ owner: Activity
+ domain_of:
+ - Activity
+ range: MoleculeAssociation
+ inlined: true
+ causal_associations:
+ name: causal_associations
+ description: The causal associations that connect this activity to other activities
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ multivalued: true
+ alias: causal_associations
+ owner: Activity
+ domain_of:
+ - Activity
+ range: CausalAssociation
+ inlined: true
+ inlined_as_list: true
+ provenances:
+ name: provenances
+ description: Provenance information for the activity
+ from_schema: https://w3id.org/gocam
+ multivalued: true
+ alias: provenances
+ owner: Activity
+ domain_of:
+ - Model
+ - Activity
+ - EvidenceItem
+ - Association
+ range: ProvenanceInfo
+ inlined: true
+ inlined_as_list: true
+
+
+An abstract grouping for different kinds of evidence-associated provenance
+URI: gocam:Association
+Name | +Cardinality and Range | +Description | +Inheritance | +
---|---|---|---|
type | +0..1 String |
++ | direct | +
evidence | +* EvidenceItem |
++ | direct | +
provenances | +* ProvenanceInfo |
++ | direct | +
Mapping Type | +Mapped Value | +
---|---|
self | +gocam:Association | +
native | +gocam:Association | +
name: Association
+description: An abstract grouping for different kinds of evidence-associated provenance
+from_schema: https://w3id.org/gocam
+abstract: true
+attributes:
+ type:
+ name: type
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ designates_type: true
+ domain_of:
+ - Association
+ - Object
+ evidence:
+ name: evidence
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ multivalued: true
+ domain_of:
+ - Association
+ range: EvidenceItem
+ inlined: true
+ provenances:
+ name: provenances
+ from_schema: https://w3id.org/gocam
+ multivalued: true
+ domain_of:
+ - Model
+ - Activity
+ - EvidenceItem
+ - Association
+ range: ProvenanceInfo
+ inlined: true
+ inlined_as_list: true
+
+
+name: Association
+description: An abstract grouping for different kinds of evidence-associated provenance
+from_schema: https://w3id.org/gocam
+abstract: true
+attributes:
+ type:
+ name: type
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ designates_type: true
+ alias: type
+ owner: Association
+ domain_of:
+ - Association
+ - Object
+ range: string
+ evidence:
+ name: evidence
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ multivalued: true
+ alias: evidence
+ owner: Association
+ domain_of:
+ - Association
+ range: EvidenceItem
+ inlined: true
+ provenances:
+ name: provenances
+ from_schema: https://w3id.org/gocam
+ multivalued: true
+ alias: provenances
+ owner: Association
+ domain_of:
+ - Model
+ - Activity
+ - EvidenceItem
+ - Association
+ range: ProvenanceInfo
+ inlined: true
+ inlined_as_list: true
+
+
+An association between an activity and a biological process term
+URI: gocam:BiologicalProcessAssociation
+Name | +Cardinality and Range | +Description | +Inheritance | +
---|---|---|---|
term | +0..1 BiologicalProcessTermObject |
+The ontology term that describes the nature of the association | +TermAssociation | +
type | +0..1 String |
++ | Association | +
evidence | +* EvidenceItem |
++ | Association | +
provenances | +* ProvenanceInfo |
++ | Association | +
used by | +used in | +type | +used | +
---|---|---|---|
Activity | +part_of | +range | +BiologicalProcessAssociation | +
Mapping Type | +Mapped Value | +
---|---|
self | +gocam:BiologicalProcessAssociation | +
native | +gocam:BiologicalProcessAssociation | +
name: BiologicalProcessAssociation
+description: An association between an activity and a biological process term
+from_schema: https://w3id.org/gocam
+is_a: TermAssociation
+slot_usage:
+ term:
+ name: term
+ domain_of:
+ - EvidenceItem
+ - EnabledByAssociation
+ - TermAssociation
+ range: BiologicalProcessTermObject
+ happens_during:
+ name: happens_during
+ description: Optional extension describing where the BP takes place
+ range: PhaseTermObject
+ part_of:
+ name: part_of
+ description: Optional extension allowing hierarchical nesting of BPs
+ range: BiologicalProcessTermObject
+
+
+name: BiologicalProcessAssociation
+description: An association between an activity and a biological process term
+from_schema: https://w3id.org/gocam
+is_a: TermAssociation
+slot_usage:
+ term:
+ name: term
+ domain_of:
+ - EvidenceItem
+ - EnabledByAssociation
+ - TermAssociation
+ range: BiologicalProcessTermObject
+ happens_during:
+ name: happens_during
+ description: Optional extension describing where the BP takes place
+ range: PhaseTermObject
+ part_of:
+ name: part_of
+ description: Optional extension allowing hierarchical nesting of BPs
+ range: BiologicalProcessTermObject
+attributes:
+ term:
+ name: term
+ description: The ontology term that describes the nature of the association
+ from_schema: https://w3id.org/gocam
+ alias: term
+ owner: BiologicalProcessAssociation
+ domain_of:
+ - EvidenceItem
+ - EnabledByAssociation
+ - TermAssociation
+ range: BiologicalProcessTermObject
+ type:
+ name: type
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ designates_type: true
+ alias: type
+ owner: BiologicalProcessAssociation
+ domain_of:
+ - Association
+ - Object
+ range: string
+ evidence:
+ name: evidence
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ multivalued: true
+ alias: evidence
+ owner: BiologicalProcessAssociation
+ domain_of:
+ - Association
+ range: EvidenceItem
+ inlined: true
+ provenances:
+ name: provenances
+ from_schema: https://w3id.org/gocam
+ multivalued: true
+ alias: provenances
+ owner: BiologicalProcessAssociation
+ domain_of:
+ - Model
+ - Activity
+ - EvidenceItem
+ - Association
+ range: ProvenanceInfo
+ inlined: true
+ inlined_as_list: true
+
+
+A term object that represents a biological process term from GO
+URI: gocam:BiologicalProcessTermObject
+Name | +Cardinality and Range | +Description | +Inheritance | +
---|---|---|---|
id | +1 Uriorcurie |
++ | Object | +
label | +0..1 String |
++ | Object | +
type | +0..1 Uriorcurie |
++ | Object | +
obsolete | +0..1 Boolean |
++ | Object | +
used by | +used in | +type | +used | +
---|---|---|---|
BiologicalProcessAssociation | +term | +range | +BiologicalProcessTermObject | +
Instances of this class should have identifiers with one of the following prefixes:
+Mapping Type | +Mapped Value | +
---|---|
self | +gocam:BiologicalProcessTermObject | +
native | +gocam:BiologicalProcessTermObject | +
name: BiologicalProcessTermObject
+id_prefixes:
+- GO
+description: A term object that represents a biological process term from GO
+from_schema: https://w3id.org/gocam
+is_a: TermObject
+
+
+name: BiologicalProcessTermObject
+id_prefixes:
+- GO
+description: A term object that represents a biological process term from GO
+from_schema: https://w3id.org/gocam
+is_a: TermObject
+attributes:
+ id:
+ name: id
+ from_schema: https://w3id.org/gocam
+ identifier: true
+ alias: id
+ owner: BiologicalProcessTermObject
+ domain_of:
+ - Model
+ - Activity
+ - Object
+ range: uriorcurie
+ required: true
+ label:
+ name: label
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ slot_uri: rdfs:label
+ alias: label
+ owner: BiologicalProcessTermObject
+ domain_of:
+ - Object
+ range: string
+ type:
+ name: type
+ from_schema: https://w3id.org/gocam
+ designates_type: true
+ alias: type
+ owner: BiologicalProcessTermObject
+ domain_of:
+ - Association
+ - Object
+ range: uriorcurie
+ obsolete:
+ name: obsolete
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ alias: obsolete
+ owner: BiologicalProcessTermObject
+ domain_of:
+ - Object
+ range: boolean
+
+
+A binary (true or false) value
+URI: xsd:boolean
+ +A causal association between two activities
+ +Name | +Cardinality and Range | +Description | +Inheritance | +
---|---|---|---|
predicate | +0..1 PredicateTermObject |
+The RO relation that represents the type of relationship | +direct | +
downstream_activity | +0..1 Activity |
+The activity unit that is downstream of this one | +direct | +
type | +0..1 String |
++ | Association | +
evidence | +* EvidenceItem |
++ | Association | +
provenances | +* ProvenanceInfo |
++ | Association | +
used by | +used in | +type | +used | +
---|---|---|---|
Activity | +causal_associations | +range | +CausalAssociation | +
Mapping Type | +Mapped Value | +
---|---|
self | +gocam:CausalAssociation | +
native | +gocam:CausalAssociation | +
name: CausalAssociation
+description: A causal association between two activities
+from_schema: https://w3id.org/gocam
+is_a: Association
+attributes:
+ predicate:
+ name: predicate
+ description: The RO relation that represents the type of relationship
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ domain_of:
+ - CausalAssociation
+ range: PredicateTermObject
+ downstream_activity:
+ name: downstream_activity
+ description: The activity unit that is downstream of this one
+ from_schema: https://w3id.org/gocam
+ aliases:
+ - object
+ rank: 1000
+ domain_of:
+ - CausalAssociation
+ range: Activity
+
+
+name: CausalAssociation
+description: A causal association between two activities
+from_schema: https://w3id.org/gocam
+is_a: Association
+attributes:
+ predicate:
+ name: predicate
+ description: The RO relation that represents the type of relationship
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ alias: predicate
+ owner: CausalAssociation
+ domain_of:
+ - CausalAssociation
+ range: PredicateTermObject
+ downstream_activity:
+ name: downstream_activity
+ description: The activity unit that is downstream of this one
+ from_schema: https://w3id.org/gocam
+ aliases:
+ - object
+ rank: 1000
+ alias: downstream_activity
+ owner: CausalAssociation
+ domain_of:
+ - CausalAssociation
+ range: Activity
+ type:
+ name: type
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ designates_type: true
+ alias: type
+ owner: CausalAssociation
+ domain_of:
+ - Association
+ - Object
+ range: string
+ evidence:
+ name: evidence
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ multivalued: true
+ alias: evidence
+ owner: CausalAssociation
+ domain_of:
+ - Association
+ range: EvidenceItem
+ inlined: true
+ provenances:
+ name: provenances
+ from_schema: https://w3id.org/gocam
+ multivalued: true
+ alias: provenances
+ owner: CausalAssociation
+ domain_of:
+ - Model
+ - Activity
+ - EvidenceItem
+ - Association
+ range: ProvenanceInfo
+ inlined: true
+ inlined_as_list: true
+
+
+URI: CausalPredicateEnum
+Value | +Meaning | +Description | +
---|---|---|
causally upstream of, positive effect | +RO:0002304 | ++ |
causally upstream of, negative effect | +RO:0002305 | ++ |
causally upstream of | +RO:0002411 | ++ |
immediately causally upstream of | +RO:0002412 | ++ |
causally upstream of or within | +RO:0002418 | ++ |
causally upstream of or within, negative effect | +RO:0004046 | ++ |
causally upstream of or within, positive effect | +RO:0004047 | ++ |
regulates | +RO:0002211 | ++ |
negatively regulates | +RO:0002212 | ++ |
positively regulates | +RO:0002213 | ++ |
name: CausalPredicateEnum
+from_schema: https://w3id.org/gocam
+rank: 1000
+permissible_values:
+ causally upstream of, positive effect:
+ text: causally upstream of, positive effect
+ meaning: RO:0002304
+ causally upstream of, negative effect:
+ text: causally upstream of, negative effect
+ meaning: RO:0002305
+ causally upstream of:
+ text: causally upstream of
+ meaning: RO:0002411
+ immediately causally upstream of:
+ text: immediately causally upstream of
+ meaning: RO:0002412
+ causally upstream of or within:
+ text: causally upstream of or within
+ meaning: RO:0002418
+ causally upstream of or within, negative effect:
+ text: causally upstream of or within, negative effect
+ meaning: RO:0004046
+ causally upstream of or within, positive effect:
+ text: causally upstream of or within, positive effect
+ meaning: RO:0004047
+ regulates:
+ text: regulates
+ meaning: RO:0002211
+ negatively regulates:
+ text: negatively regulates
+ meaning: RO:0002212
+ positively regulates:
+ text: positively regulates
+ meaning: RO:0002213
+
+
+
+An association between an activity and a cell type term
+URI: gocam:CellTypeAssociation
+Name | +Cardinality and Range | +Description | +Inheritance | +
---|---|---|---|
term | +0..1 CellTypeTermObject |
+The ontology term that describes the nature of the association | +TermAssociation | +
type | +0..1 String |
++ | Association | +
evidence | +* EvidenceItem |
++ | Association | +
provenances | +* ProvenanceInfo |
++ | Association | +
Mapping Type | +Mapped Value | +
---|---|
self | +gocam:CellTypeAssociation | +
native | +gocam:CellTypeAssociation | +
name: CellTypeAssociation
+description: An association between an activity and a cell type term
+from_schema: https://w3id.org/gocam
+is_a: TermAssociation
+slot_usage:
+ term:
+ name: term
+ domain_of:
+ - EvidenceItem
+ - EnabledByAssociation
+ - TermAssociation
+ range: CellTypeTermObject
+ part_of:
+ name: part_of
+ range: GrossAnatomyAssociation
+
+
+name: CellTypeAssociation
+description: An association between an activity and a cell type term
+from_schema: https://w3id.org/gocam
+is_a: TermAssociation
+slot_usage:
+ term:
+ name: term
+ domain_of:
+ - EvidenceItem
+ - EnabledByAssociation
+ - TermAssociation
+ range: CellTypeTermObject
+ part_of:
+ name: part_of
+ range: GrossAnatomyAssociation
+attributes:
+ term:
+ name: term
+ description: The ontology term that describes the nature of the association
+ from_schema: https://w3id.org/gocam
+ alias: term
+ owner: CellTypeAssociation
+ domain_of:
+ - EvidenceItem
+ - EnabledByAssociation
+ - TermAssociation
+ range: CellTypeTermObject
+ type:
+ name: type
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ designates_type: true
+ alias: type
+ owner: CellTypeAssociation
+ domain_of:
+ - Association
+ - Object
+ range: string
+ evidence:
+ name: evidence
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ multivalued: true
+ alias: evidence
+ owner: CellTypeAssociation
+ domain_of:
+ - Association
+ range: EvidenceItem
+ inlined: true
+ provenances:
+ name: provenances
+ from_schema: https://w3id.org/gocam
+ multivalued: true
+ alias: provenances
+ owner: CellTypeAssociation
+ domain_of:
+ - Model
+ - Activity
+ - EvidenceItem
+ - Association
+ range: ProvenanceInfo
+ inlined: true
+ inlined_as_list: true
+
+
+A term object that represents a cell type term from CL
+ +Name | +Cardinality and Range | +Description | +Inheritance | +
---|---|---|---|
id | +1 Uriorcurie |
++ | Object | +
label | +0..1 String |
++ | Object | +
type | +0..1 Uriorcurie |
++ | Object | +
obsolete | +0..1 Boolean |
++ | Object | +
used by | +used in | +type | +used | +
---|---|---|---|
CellTypeAssociation | +term | +range | +CellTypeTermObject | +
Instances of this class should have identifiers with one of the following prefixes:
+CL
+PO
+FAO
+DDANAT
+Mapping Type | +Mapped Value | +
---|---|
self | +gocam:CellTypeTermObject | +
native | +gocam:CellTypeTermObject | +
name: CellTypeTermObject
+id_prefixes:
+- CL
+- PO
+- FAO
+- DDANAT
+description: A term object that represents a cell type term from CL
+from_schema: https://w3id.org/gocam
+is_a: TermObject
+
+
+name: CellTypeTermObject
+id_prefixes:
+- CL
+- PO
+- FAO
+- DDANAT
+description: A term object that represents a cell type term from CL
+from_schema: https://w3id.org/gocam
+is_a: TermObject
+attributes:
+ id:
+ name: id
+ from_schema: https://w3id.org/gocam
+ identifier: true
+ alias: id
+ owner: CellTypeTermObject
+ domain_of:
+ - Model
+ - Activity
+ - Object
+ range: uriorcurie
+ required: true
+ label:
+ name: label
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ slot_uri: rdfs:label
+ alias: label
+ owner: CellTypeTermObject
+ domain_of:
+ - Object
+ range: string
+ type:
+ name: type
+ from_schema: https://w3id.org/gocam
+ designates_type: true
+ alias: type
+ owner: CellTypeTermObject
+ domain_of:
+ - Association
+ - Object
+ range: uriorcurie
+ obsolete:
+ name: obsolete
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ alias: obsolete
+ owner: CellTypeTermObject
+ domain_of:
+ - Object
+ range: boolean
+
+
+An association between an activity and a cellular anatomical entity term
+URI: gocam:CellularAnatomicalEntityAssociation
+Name | +Cardinality and Range | +Description | +Inheritance | +
---|---|---|---|
term | +0..1 CellularAnatomicalEntityTermObject |
+The ontology term that describes the nature of the association | +TermAssociation | +
type | +0..1 String |
++ | Association | +
evidence | +* EvidenceItem |
++ | Association | +
provenances | +* ProvenanceInfo |
++ | Association | +
used by | +used in | +type | +used | +
---|---|---|---|
Activity | +occurs_in | +range | +CellularAnatomicalEntityAssociation | +
Mapping Type | +Mapped Value | +
---|---|
self | +gocam:CellularAnatomicalEntityAssociation | +
native | +gocam:CellularAnatomicalEntityAssociation | +
name: CellularAnatomicalEntityAssociation
+description: An association between an activity and a cellular anatomical entity term
+from_schema: https://w3id.org/gocam
+is_a: TermAssociation
+slot_usage:
+ term:
+ name: term
+ domain_of:
+ - EvidenceItem
+ - EnabledByAssociation
+ - TermAssociation
+ range: CellularAnatomicalEntityTermObject
+ part_of:
+ name: part_of
+ range: CellTypeAssociation
+
+
+name: CellularAnatomicalEntityAssociation
+description: An association between an activity and a cellular anatomical entity term
+from_schema: https://w3id.org/gocam
+is_a: TermAssociation
+slot_usage:
+ term:
+ name: term
+ domain_of:
+ - EvidenceItem
+ - EnabledByAssociation
+ - TermAssociation
+ range: CellularAnatomicalEntityTermObject
+ part_of:
+ name: part_of
+ range: CellTypeAssociation
+attributes:
+ term:
+ name: term
+ description: The ontology term that describes the nature of the association
+ from_schema: https://w3id.org/gocam
+ alias: term
+ owner: CellularAnatomicalEntityAssociation
+ domain_of:
+ - EvidenceItem
+ - EnabledByAssociation
+ - TermAssociation
+ range: CellularAnatomicalEntityTermObject
+ type:
+ name: type
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ designates_type: true
+ alias: type
+ owner: CellularAnatomicalEntityAssociation
+ domain_of:
+ - Association
+ - Object
+ range: string
+ evidence:
+ name: evidence
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ multivalued: true
+ alias: evidence
+ owner: CellularAnatomicalEntityAssociation
+ domain_of:
+ - Association
+ range: EvidenceItem
+ inlined: true
+ provenances:
+ name: provenances
+ from_schema: https://w3id.org/gocam
+ multivalued: true
+ alias: provenances
+ owner: CellularAnatomicalEntityAssociation
+ domain_of:
+ - Model
+ - Activity
+ - EvidenceItem
+ - Association
+ range: ProvenanceInfo
+ inlined: true
+ inlined_as_list: true
+
+
+A term object that represents a cellular anatomical entity term from GO
+URI: gocam:CellularAnatomicalEntityTermObject
+Name | +Cardinality and Range | +Description | +Inheritance | +
---|---|---|---|
id | +1 Uriorcurie |
++ | Object | +
label | +0..1 String |
++ | Object | +
type | +0..1 Uriorcurie |
++ | Object | +
obsolete | +0..1 Boolean |
++ | Object | +
used by | +used in | +type | +used | +
---|---|---|---|
CellularAnatomicalEntityAssociation | +term | +range | +CellularAnatomicalEntityTermObject | +
Instances of this class should have identifiers with one of the following prefixes:
+Mapping Type | +Mapped Value | +
---|---|
self | +gocam:CellularAnatomicalEntityTermObject | +
native | +gocam:CellularAnatomicalEntityTermObject | +
name: CellularAnatomicalEntityTermObject
+id_prefixes:
+- GO
+description: A term object that represents a cellular anatomical entity term from
+ GO
+from_schema: https://w3id.org/gocam
+is_a: TermObject
+
+
+name: CellularAnatomicalEntityTermObject
+id_prefixes:
+- GO
+description: A term object that represents a cellular anatomical entity term from
+ GO
+from_schema: https://w3id.org/gocam
+is_a: TermObject
+attributes:
+ id:
+ name: id
+ from_schema: https://w3id.org/gocam
+ identifier: true
+ alias: id
+ owner: CellularAnatomicalEntityTermObject
+ domain_of:
+ - Model
+ - Activity
+ - Object
+ range: uriorcurie
+ required: true
+ label:
+ name: label
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ slot_uri: rdfs:label
+ alias: label
+ owner: CellularAnatomicalEntityTermObject
+ domain_of:
+ - Object
+ range: string
+ type:
+ name: type
+ from_schema: https://w3id.org/gocam
+ designates_type: true
+ alias: type
+ owner: CellularAnatomicalEntityTermObject
+ domain_of:
+ - Association
+ - Object
+ range: uriorcurie
+ obsolete:
+ name: obsolete
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ alias: obsolete
+ owner: CellularAnatomicalEntityTermObject
+ domain_of:
+ - Object
+ range: boolean
+
+
+a compact URI
+URI: xsd:string
+ +Either a date or a datetime
+ + +The combination of a date and time
+URI: xsd:dateTime
+ +A real number with arbitrary precision that conforms to the xsd:decimal specification
+URI: xsd:decimal
+ +A real number that conforms to the xsd:double specification
+URI: xsd:double
+ +An association between an activity and the gene product or complex that carries it out
+URI: gocam:EnabledByAssociation
+Name | +Cardinality and Range | +Description | +Inheritance | +
---|---|---|---|
term | +0..1 InformationBiomacromoleculeTermObject |
+The gene product or complex that carries out the activity | +direct | +
type | +0..1 String |
++ | Association | +
evidence | +* EvidenceItem |
++ | Association | +
provenances | +* ProvenanceInfo |
++ | Association | +
used by | +used in | +type | +used | +
---|---|---|---|
Activity | +enabled_by | +range | +EnabledByAssociation | +
Mapping Type | +Mapped Value | +
---|---|
self | +gocam:EnabledByAssociation | +
native | +gocam:EnabledByAssociation | +
name: EnabledByAssociation
+description: An association between an activity and the gene product or complex that
+ carries it out
+from_schema: https://w3id.org/gocam
+is_a: Association
+abstract: true
+attributes:
+ term:
+ name: term
+ description: The gene product or complex that carries out the activity
+ from_schema: https://w3id.org/gocam
+ domain_of:
+ - EvidenceItem
+ - EnabledByAssociation
+ - TermAssociation
+ range: InformationBiomacromoleculeTermObject
+
+
+name: EnabledByAssociation
+description: An association between an activity and the gene product or complex that
+ carries it out
+from_schema: https://w3id.org/gocam
+is_a: Association
+abstract: true
+attributes:
+ term:
+ name: term
+ description: The gene product or complex that carries out the activity
+ from_schema: https://w3id.org/gocam
+ alias: term
+ owner: EnabledByAssociation
+ domain_of:
+ - EvidenceItem
+ - EnabledByAssociation
+ - TermAssociation
+ range: InformationBiomacromoleculeTermObject
+ type:
+ name: type
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ designates_type: true
+ alias: type
+ owner: EnabledByAssociation
+ domain_of:
+ - Association
+ - Object
+ range: string
+ evidence:
+ name: evidence
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ multivalued: true
+ alias: evidence
+ owner: EnabledByAssociation
+ domain_of:
+ - Association
+ range: EvidenceItem
+ inlined: true
+ provenances:
+ name: provenances
+ from_schema: https://w3id.org/gocam
+ multivalued: true
+ alias: provenances
+ owner: EnabledByAssociation
+ domain_of:
+ - Model
+ - Activity
+ - EvidenceItem
+ - Association
+ range: ProvenanceInfo
+ inlined: true
+ inlined_as_list: true
+
+
+An association between an activity and a gene product
+URI: gocam:EnabledByGeneProductAssociation
+Name | +Cardinality and Range | +Description | +Inheritance | +
---|---|---|---|
term | +0..1 GeneProductTermObject |
+The gene product or complex that carries out the activity | +EnabledByAssociation | +
type | +0..1 String |
++ | Association | +
evidence | +* EvidenceItem |
++ | Association | +
provenances | +* ProvenanceInfo |
++ | Association | +
Mapping Type | +Mapped Value | +
---|---|
self | +gocam:EnabledByGeneProductAssociation | +
native | +gocam:EnabledByGeneProductAssociation | +
name: EnabledByGeneProductAssociation
+description: An association between an activity and a gene product
+from_schema: https://w3id.org/gocam
+is_a: EnabledByAssociation
+slot_usage:
+ term:
+ name: term
+ domain_of:
+ - EvidenceItem
+ - EnabledByAssociation
+ - TermAssociation
+ range: GeneProductTermObject
+
+
+name: EnabledByGeneProductAssociation
+description: An association between an activity and a gene product
+from_schema: https://w3id.org/gocam
+is_a: EnabledByAssociation
+slot_usage:
+ term:
+ name: term
+ domain_of:
+ - EvidenceItem
+ - EnabledByAssociation
+ - TermAssociation
+ range: GeneProductTermObject
+attributes:
+ term:
+ name: term
+ description: The gene product or complex that carries out the activity
+ from_schema: https://w3id.org/gocam
+ alias: term
+ owner: EnabledByGeneProductAssociation
+ domain_of:
+ - EvidenceItem
+ - EnabledByAssociation
+ - TermAssociation
+ range: GeneProductTermObject
+ type:
+ name: type
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ designates_type: true
+ alias: type
+ owner: EnabledByGeneProductAssociation
+ domain_of:
+ - Association
+ - Object
+ range: string
+ evidence:
+ name: evidence
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ multivalued: true
+ alias: evidence
+ owner: EnabledByGeneProductAssociation
+ domain_of:
+ - Association
+ range: EvidenceItem
+ inlined: true
+ provenances:
+ name: provenances
+ from_schema: https://w3id.org/gocam
+ multivalued: true
+ alias: provenances
+ owner: EnabledByGeneProductAssociation
+ domain_of:
+ - Model
+ - Activity
+ - EvidenceItem
+ - Association
+ range: ProvenanceInfo
+ inlined: true
+ inlined_as_list: true
+
+
+An association between an activity and a protein complex
+URI: gocam:EnabledByProteinComplexAssociation
+Name | +Cardinality and Range | +Description | +Inheritance | +
---|---|---|---|
members | +* GeneProductTermObject |
+The gene products that are part of the complex | +direct | +
term | +0..1 ProteinComplexTermObject |
+The gene product or complex that carries out the activity | +EnabledByAssociation | +
type | +0..1 String |
++ | Association | +
evidence | +* EvidenceItem |
++ | Association | +
provenances | +* ProvenanceInfo |
++ | Association | +
Mapping Type | +Mapped Value | +
---|---|
self | +gocam:EnabledByProteinComplexAssociation | +
native | +gocam:EnabledByProteinComplexAssociation | +
name: EnabledByProteinComplexAssociation
+description: An association between an activity and a protein complex
+from_schema: https://w3id.org/gocam
+is_a: EnabledByAssociation
+slot_usage:
+ term:
+ name: term
+ domain_of:
+ - EvidenceItem
+ - EnabledByAssociation
+ - TermAssociation
+ range: ProteinComplexTermObject
+attributes:
+ members:
+ name: members
+ description: The gene products that are part of the complex
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ multivalued: true
+ domain_of:
+ - EnabledByProteinComplexAssociation
+ range: GeneProductTermObject
+
+
+name: EnabledByProteinComplexAssociation
+description: An association between an activity and a protein complex
+from_schema: https://w3id.org/gocam
+is_a: EnabledByAssociation
+slot_usage:
+ term:
+ name: term
+ domain_of:
+ - EvidenceItem
+ - EnabledByAssociation
+ - TermAssociation
+ range: ProteinComplexTermObject
+attributes:
+ members:
+ name: members
+ description: The gene products that are part of the complex
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ multivalued: true
+ alias: members
+ owner: EnabledByProteinComplexAssociation
+ domain_of:
+ - EnabledByProteinComplexAssociation
+ range: GeneProductTermObject
+ term:
+ name: term
+ description: The gene product or complex that carries out the activity
+ from_schema: https://w3id.org/gocam
+ alias: term
+ owner: EnabledByProteinComplexAssociation
+ domain_of:
+ - EvidenceItem
+ - EnabledByAssociation
+ - TermAssociation
+ range: ProteinComplexTermObject
+ type:
+ name: type
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ designates_type: true
+ alias: type
+ owner: EnabledByProteinComplexAssociation
+ domain_of:
+ - Association
+ - Object
+ range: string
+ evidence:
+ name: evidence
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ multivalued: true
+ alias: evidence
+ owner: EnabledByProteinComplexAssociation
+ domain_of:
+ - Association
+ range: EvidenceItem
+ inlined: true
+ provenances:
+ name: provenances
+ from_schema: https://w3id.org/gocam
+ multivalued: true
+ alias: provenances
+ owner: EnabledByProteinComplexAssociation
+ domain_of:
+ - Model
+ - Activity
+ - EvidenceItem
+ - Association
+ range: ProvenanceInfo
+ inlined: true
+ inlined_as_list: true
+
+
+An individual piece of evidence that is associated with an assertion in a model
+URI: gocam:EvidenceItem
+Name | +Cardinality and Range | +Description | +Inheritance | +
---|---|---|---|
term | +0..1 EvidenceTermObject |
+The ECO term representing the type of evidence | +direct | +
reference | +0..1 PublicationObject |
+The publication of reference that describes the evidence | +direct | +
with_objects | +* Object |
+Supporting database entities or terms | +direct | +
provenances | +* ProvenanceInfo |
+Provenance about the assertion, e | +direct | +
used by | +used in | +type | +used | +
---|---|---|---|
Association | +evidence | +range | +EvidenceItem | +
EnabledByAssociation | +evidence | +range | +EvidenceItem | +
EnabledByGeneProductAssociation | +evidence | +range | +EvidenceItem | +
EnabledByProteinComplexAssociation | +evidence | +range | +EvidenceItem | +
CausalAssociation | +evidence | +range | +EvidenceItem | +
TermAssociation | +evidence | +range | +EvidenceItem | +
MolecularFunctionAssociation | +evidence | +range | +EvidenceItem | +
BiologicalProcessAssociation | +evidence | +range | +EvidenceItem | +
CellularAnatomicalEntityAssociation | +evidence | +range | +EvidenceItem | +
CellTypeAssociation | +evidence | +range | +EvidenceItem | +
GrossAnatomyAssociation | +evidence | +range | +EvidenceItem | +
MoleculeAssociation | +evidence | +range | +EvidenceItem | +
Mapping Type | +Mapped Value | +
---|---|
self | +gocam:EvidenceItem | +
native | +gocam:EvidenceItem | +
name: EvidenceItem
+description: An individual piece of evidence that is associated with an assertion
+ in a model
+from_schema: https://w3id.org/gocam
+attributes:
+ term:
+ name: term
+ description: The ECO term representing the type of evidence
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ domain_of:
+ - EvidenceItem
+ - EnabledByAssociation
+ - TermAssociation
+ range: EvidenceTermObject
+ reference:
+ name: reference
+ description: The publication of reference that describes the evidence
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ domain_of:
+ - EvidenceItem
+ range: PublicationObject
+ with_objects:
+ name: with_objects
+ description: Supporting database entities or terms
+ from_schema: https://w3id.org/gocam
+ aliases:
+ - with
+ - with/from
+ rank: 1000
+ multivalued: true
+ domain_of:
+ - EvidenceItem
+ range: Object
+ provenances:
+ name: provenances
+ description: Provenance about the assertion, e.g. who made it
+ from_schema: https://w3id.org/gocam
+ multivalued: true
+ domain_of:
+ - Model
+ - Activity
+ - EvidenceItem
+ - Association
+ range: ProvenanceInfo
+ inlined: true
+ inlined_as_list: true
+
+
+name: EvidenceItem
+description: An individual piece of evidence that is associated with an assertion
+ in a model
+from_schema: https://w3id.org/gocam
+attributes:
+ term:
+ name: term
+ description: The ECO term representing the type of evidence
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ alias: term
+ owner: EvidenceItem
+ domain_of:
+ - EvidenceItem
+ - EnabledByAssociation
+ - TermAssociation
+ range: EvidenceTermObject
+ reference:
+ name: reference
+ description: The publication of reference that describes the evidence
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ alias: reference
+ owner: EvidenceItem
+ domain_of:
+ - EvidenceItem
+ range: PublicationObject
+ with_objects:
+ name: with_objects
+ description: Supporting database entities or terms
+ from_schema: https://w3id.org/gocam
+ aliases:
+ - with
+ - with/from
+ rank: 1000
+ multivalued: true
+ alias: with_objects
+ owner: EvidenceItem
+ domain_of:
+ - EvidenceItem
+ range: Object
+ provenances:
+ name: provenances
+ description: Provenance about the assertion, e.g. who made it
+ from_schema: https://w3id.org/gocam
+ multivalued: true
+ alias: provenances
+ owner: EvidenceItem
+ domain_of:
+ - Model
+ - Activity
+ - EvidenceItem
+ - Association
+ range: ProvenanceInfo
+ inlined: true
+ inlined_as_list: true
+
+
+A term object that represents an evidence term from ECO
+ +Name | +Cardinality and Range | +Description | +Inheritance | +
---|---|---|---|
id | +1 Uriorcurie |
++ | Object | +
label | +0..1 String |
++ | Object | +
type | +0..1 Uriorcurie |
++ | Object | +
obsolete | +0..1 Boolean |
++ | Object | +
used by | +used in | +type | +used | +
---|---|---|---|
EvidenceItem | +term | +range | +EvidenceTermObject | +
Instances of this class should have identifiers with one of the following prefixes:
+Mapping Type | +Mapped Value | +
---|---|
self | +gocam:EvidenceTermObject | +
native | +gocam:EvidenceTermObject | +
name: EvidenceTermObject
+id_prefixes:
+- ECO
+description: A term object that represents an evidence term from ECO
+from_schema: https://w3id.org/gocam
+is_a: TermObject
+
+
+name: EvidenceTermObject
+id_prefixes:
+- ECO
+description: A term object that represents an evidence term from ECO
+from_schema: https://w3id.org/gocam
+is_a: TermObject
+attributes:
+ id:
+ name: id
+ from_schema: https://w3id.org/gocam
+ identifier: true
+ alias: id
+ owner: EvidenceTermObject
+ domain_of:
+ - Model
+ - Activity
+ - Object
+ range: uriorcurie
+ required: true
+ label:
+ name: label
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ slot_uri: rdfs:label
+ alias: label
+ owner: EvidenceTermObject
+ domain_of:
+ - Object
+ range: string
+ type:
+ name: type
+ from_schema: https://w3id.org/gocam
+ designates_type: true
+ alias: type
+ owner: EvidenceTermObject
+ domain_of:
+ - Association
+ - Object
+ range: uriorcurie
+ obsolete:
+ name: obsolete
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ alias: obsolete
+ owner: EvidenceTermObject
+ domain_of:
+ - Object
+ range: boolean
+
+
+A term object that represents a gene product term from GO or UniProtKB
+URI: gocam:GeneProductTermObject
+Name | +Cardinality and Range | +Description | +Inheritance | +
---|---|---|---|
id | +1 Uriorcurie |
++ | Object | +
label | +0..1 String |
++ | Object | +
type | +0..1 Uriorcurie |
++ | Object | +
obsolete | +0..1 Boolean |
++ | Object | +
used by | +used in | +type | +used | +
---|---|---|---|
EnabledByGeneProductAssociation | +term | +range | +GeneProductTermObject | +
EnabledByProteinComplexAssociation | +members | +range | +GeneProductTermObject | +
Mapping Type | +Mapped Value | +
---|---|
self | +gocam:GeneProductTermObject | +
native | +gocam:GeneProductTermObject | +
name: GeneProductTermObject
+description: A term object that represents a gene product term from GO or UniProtKB
+from_schema: https://w3id.org/gocam
+is_a: InformationBiomacromoleculeTermObject
+
+
+name: GeneProductTermObject
+description: A term object that represents a gene product term from GO or UniProtKB
+from_schema: https://w3id.org/gocam
+is_a: InformationBiomacromoleculeTermObject
+attributes:
+ id:
+ name: id
+ from_schema: https://w3id.org/gocam
+ identifier: true
+ alias: id
+ owner: GeneProductTermObject
+ domain_of:
+ - Model
+ - Activity
+ - Object
+ range: uriorcurie
+ required: true
+ label:
+ name: label
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ slot_uri: rdfs:label
+ alias: label
+ owner: GeneProductTermObject
+ domain_of:
+ - Object
+ range: string
+ type:
+ name: type
+ from_schema: https://w3id.org/gocam
+ designates_type: true
+ alias: type
+ owner: GeneProductTermObject
+ domain_of:
+ - Association
+ - Object
+ range: uriorcurie
+ obsolete:
+ name: obsolete
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ alias: obsolete
+ owner: GeneProductTermObject
+ domain_of:
+ - Object
+ range: boolean
+
+
+A term object that represents a gross anatomical structure term from UBERON
+URI: gocam:GrossAnatomicalStructureTermObject
+Name | +Cardinality and Range | +Description | +Inheritance | +
---|---|---|---|
id | +1 Uriorcurie |
++ | Object | +
label | +0..1 String |
++ | Object | +
type | +0..1 Uriorcurie |
++ | Object | +
obsolete | +0..1 Boolean |
++ | Object | +
used by | +used in | +type | +used | +
---|---|---|---|
GrossAnatomyAssociation | +term | +range | +GrossAnatomicalStructureTermObject | +
Instances of this class should have identifiers with one of the following prefixes:
+UBERON
+PO
+FAO
+DDANAT
+Mapping Type | +Mapped Value | +
---|---|
self | +gocam:GrossAnatomicalStructureTermObject | +
native | +gocam:GrossAnatomicalStructureTermObject | +
name: GrossAnatomicalStructureTermObject
+id_prefixes:
+- UBERON
+- PO
+- FAO
+- DDANAT
+description: A term object that represents a gross anatomical structure term from
+ UBERON
+from_schema: https://w3id.org/gocam
+is_a: TermObject
+
+
+name: GrossAnatomicalStructureTermObject
+id_prefixes:
+- UBERON
+- PO
+- FAO
+- DDANAT
+description: A term object that represents a gross anatomical structure term from
+ UBERON
+from_schema: https://w3id.org/gocam
+is_a: TermObject
+attributes:
+ id:
+ name: id
+ from_schema: https://w3id.org/gocam
+ identifier: true
+ alias: id
+ owner: GrossAnatomicalStructureTermObject
+ domain_of:
+ - Model
+ - Activity
+ - Object
+ range: uriorcurie
+ required: true
+ label:
+ name: label
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ slot_uri: rdfs:label
+ alias: label
+ owner: GrossAnatomicalStructureTermObject
+ domain_of:
+ - Object
+ range: string
+ type:
+ name: type
+ from_schema: https://w3id.org/gocam
+ designates_type: true
+ alias: type
+ owner: GrossAnatomicalStructureTermObject
+ domain_of:
+ - Association
+ - Object
+ range: uriorcurie
+ obsolete:
+ name: obsolete
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ alias: obsolete
+ owner: GrossAnatomicalStructureTermObject
+ domain_of:
+ - Object
+ range: boolean
+
+
+An association between an activity and a gross anatomical structure term
+URI: gocam:GrossAnatomyAssociation
+Name | +Cardinality and Range | +Description | +Inheritance | +
---|---|---|---|
term | +0..1 GrossAnatomicalStructureTermObject |
+The ontology term that describes the nature of the association | +TermAssociation | +
type | +0..1 String |
++ | Association | +
evidence | +* EvidenceItem |
++ | Association | +
provenances | +* ProvenanceInfo |
++ | Association | +
Mapping Type | +Mapped Value | +
---|---|
self | +gocam:GrossAnatomyAssociation | +
native | +gocam:GrossAnatomyAssociation | +
name: GrossAnatomyAssociation
+description: An association between an activity and a gross anatomical structure term
+from_schema: https://w3id.org/gocam
+is_a: TermAssociation
+slot_usage:
+ term:
+ name: term
+ domain_of:
+ - EvidenceItem
+ - EnabledByAssociation
+ - TermAssociation
+ range: GrossAnatomicalStructureTermObject
+ part_of:
+ name: part_of
+ range: GrossAnatomyAssociation
+
+
+name: GrossAnatomyAssociation
+description: An association between an activity and a gross anatomical structure term
+from_schema: https://w3id.org/gocam
+is_a: TermAssociation
+slot_usage:
+ term:
+ name: term
+ domain_of:
+ - EvidenceItem
+ - EnabledByAssociation
+ - TermAssociation
+ range: GrossAnatomicalStructureTermObject
+ part_of:
+ name: part_of
+ range: GrossAnatomyAssociation
+attributes:
+ term:
+ name: term
+ description: The ontology term that describes the nature of the association
+ from_schema: https://w3id.org/gocam
+ alias: term
+ owner: GrossAnatomyAssociation
+ domain_of:
+ - EvidenceItem
+ - EnabledByAssociation
+ - TermAssociation
+ range: GrossAnatomicalStructureTermObject
+ type:
+ name: type
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ designates_type: true
+ alias: type
+ owner: GrossAnatomyAssociation
+ domain_of:
+ - Association
+ - Object
+ range: string
+ evidence:
+ name: evidence
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ multivalued: true
+ alias: evidence
+ owner: GrossAnatomyAssociation
+ domain_of:
+ - Association
+ range: EvidenceItem
+ inlined: true
+ provenances:
+ name: provenances
+ from_schema: https://w3id.org/gocam
+ multivalued: true
+ alias: provenances
+ owner: GrossAnatomyAssociation
+ domain_of:
+ - Model
+ - Activity
+ - EvidenceItem
+ - Association
+ range: ProvenanceInfo
+ inlined: true
+ inlined_as_list: true
+
+
+URI: InformationBiomacromoleculeCategory
+Value | +Meaning | +Description | +
---|---|---|
GeneOrReferenceProtein | +biolink.GeneOrGeneProduct | ++ |
ProteinIsoform | +None | ++ |
MacromolecularComplex | +None | ++ |
Unknown | +None | ++ |
name: InformationBiomacromoleculeCategory
+from_schema: https://w3id.org/gocam
+rank: 1000
+permissible_values:
+ GeneOrReferenceProtein:
+ text: GeneOrReferenceProtein
+ meaning: biolink.GeneOrGeneProduct
+ ProteinIsoform:
+ text: ProteinIsoform
+ MacromolecularComplex:
+ text: MacromolecularComplex
+ Unknown:
+ text: Unknown
+
+
+
+An abstract class for all information biomacromolecule term objects
+URI: gocam:InformationBiomacromoleculeTermObject
+Name | +Cardinality and Range | +Description | +Inheritance | +
---|---|---|---|
id | +1 Uriorcurie |
++ | Object | +
label | +0..1 String |
++ | Object | +
type | +0..1 Uriorcurie |
++ | Object | +
obsolete | +0..1 Boolean |
++ | Object | +
used by | +used in | +type | +used | +
---|---|---|---|
EnabledByAssociation | +term | +range | +InformationBiomacromoleculeTermObject | +
Mapping Type | +Mapped Value | +
---|---|
self | +gocam:InformationBiomacromoleculeTermObject | +
native | +gocam:InformationBiomacromoleculeTermObject | +
name: InformationBiomacromoleculeTermObject
+description: An abstract class for all information biomacromolecule term objects
+from_schema: https://w3id.org/gocam
+is_a: TermObject
+abstract: true
+
+
+name: InformationBiomacromoleculeTermObject
+description: An abstract class for all information biomacromolecule term objects
+from_schema: https://w3id.org/gocam
+is_a: TermObject
+abstract: true
+attributes:
+ id:
+ name: id
+ from_schema: https://w3id.org/gocam
+ identifier: true
+ alias: id
+ owner: InformationBiomacromoleculeTermObject
+ domain_of:
+ - Model
+ - Activity
+ - Object
+ range: uriorcurie
+ required: true
+ label:
+ name: label
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ slot_uri: rdfs:label
+ alias: label
+ owner: InformationBiomacromoleculeTermObject
+ domain_of:
+ - Object
+ range: string
+ type:
+ name: type
+ from_schema: https://w3id.org/gocam
+ designates_type: true
+ alias: type
+ owner: InformationBiomacromoleculeTermObject
+ domain_of:
+ - Association
+ - Object
+ range: uriorcurie
+ obsolete:
+ name: obsolete
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ alias: obsolete
+ owner: InformationBiomacromoleculeTermObject
+ domain_of:
+ - Object
+ range: boolean
+
+
+An integer
+URI: xsd:integer
+ +A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.
+URI: xsd:string
+ +A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.
+URI: xsd:string
+ +A model of a biological program consisting of a set of causally connected activities
+URI: gocam:Model
+Name | +Cardinality and Range | +Description | +Inheritance | +
---|---|---|---|
id | +1 Uriorcurie |
+The identifier of the model | +direct | +
title | +0..1 String |
+The human-readable descriptive title of the model | +direct | +
taxon | +0..1 TaxonTermObject |
+The primary taxon that the model is about | +direct | +
status | +0..1 ModelStateEnum |
+The status of the model | +direct | +
comments | +* String |
+Comments about the model | +direct | +
activities | +* Activity |
+All of the activities that are part of the model | +direct | +
objects | +* Object |
+All of the objects that are part of the model | +direct | +
provenances | +* ProvenanceInfo |
+Model-level provenance information | +direct | +
Mapping Type | +Mapped Value | +
---|---|
self | +gocam:Model | +
native | +gocam:Model | +
name: Model
+description: A model of a biological program consisting of a set of causally connected
+ activities
+from_schema: https://w3id.org/gocam
+attributes:
+ id:
+ name: id
+ description: The identifier of the model. Should be in gocam namespace.
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ identifier: true
+ domain_of:
+ - Model
+ - Activity
+ - Object
+ range: uriorcurie
+ required: true
+ title:
+ name: title
+ description: The human-readable descriptive title of the model
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ slot_uri: dct:title
+ domain_of:
+ - Model
+ taxon:
+ name: taxon
+ description: The primary taxon that the model is about
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ domain_of:
+ - Model
+ range: TaxonTermObject
+ status:
+ name: status
+ description: The status of the model
+ from_schema: https://w3id.org/gocam
+ aliases:
+ - model state
+ rank: 1000
+ slot_uri: pav:status
+ domain_of:
+ - Model
+ range: ModelStateEnum
+ comments:
+ name: comments
+ description: Comments about the model
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ slot_uri: rdfs:comment
+ multivalued: true
+ domain_of:
+ - Model
+ activities:
+ name: activities
+ description: All of the activities that are part of the model
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ multivalued: true
+ domain_of:
+ - Model
+ range: Activity
+ inlined: true
+ inlined_as_list: true
+ objects:
+ name: objects
+ description: All of the objects that are part of the model. This includes terms
+ as well as publications and database objects like gene. This is not strictly
+ part of the data managed by the model, it is for convenience, and should be
+ refreshed from outside.
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ multivalued: true
+ domain_of:
+ - Model
+ range: Object
+ inlined: true
+ inlined_as_list: true
+ provenances:
+ name: provenances
+ description: Model-level provenance information
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ multivalued: true
+ domain_of:
+ - Model
+ - Activity
+ - EvidenceItem
+ - Association
+ range: ProvenanceInfo
+ inlined: true
+ inlined_as_list: true
+
+
+name: Model
+description: A model of a biological program consisting of a set of causally connected
+ activities
+from_schema: https://w3id.org/gocam
+attributes:
+ id:
+ name: id
+ description: The identifier of the model. Should be in gocam namespace.
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ identifier: true
+ alias: id
+ owner: Model
+ domain_of:
+ - Model
+ - Activity
+ - Object
+ range: uriorcurie
+ title:
+ name: title
+ description: The human-readable descriptive title of the model
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ slot_uri: dct:title
+ alias: title
+ owner: Model
+ domain_of:
+ - Model
+ range: string
+ taxon:
+ name: taxon
+ description: The primary taxon that the model is about
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ alias: taxon
+ owner: Model
+ domain_of:
+ - Model
+ range: TaxonTermObject
+ status:
+ name: status
+ description: The status of the model
+ from_schema: https://w3id.org/gocam
+ aliases:
+ - model state
+ rank: 1000
+ slot_uri: pav:status
+ alias: status
+ owner: Model
+ domain_of:
+ - Model
+ range: ModelStateEnum
+ comments:
+ name: comments
+ description: Comments about the model
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ slot_uri: rdfs:comment
+ multivalued: true
+ alias: comments
+ owner: Model
+ domain_of:
+ - Model
+ range: string
+ activities:
+ name: activities
+ description: All of the activities that are part of the model
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ multivalued: true
+ alias: activities
+ owner: Model
+ domain_of:
+ - Model
+ range: Activity
+ inlined_as_list: true
+ objects:
+ name: objects
+ description: All of the objects that are part of the model. This includes terms
+ as well as publications and database objects like gene. This is not strictly
+ part of the data managed by the model, it is for convenience, and should be
+ refreshed from outside.
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ multivalued: true
+ alias: objects
+ owner: Model
+ domain_of:
+ - Model
+ range: Object
+ inlined_as_list: true
+ provenances:
+ name: provenances
+ description: Model-level provenance information
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ multivalued: true
+ alias: provenances
+ owner: Model
+ domain_of:
+ - Model
+ - Activity
+ - EvidenceItem
+ - Association
+ range: ProvenanceInfo
+ inlined_as_list: true
+
+
+Status of a model
+URI: ModelStateEnum
+Value | +Meaning | +Description | +
---|---|---|
production | +None | ++ |
development | +None | ++ |
Name | +Description | +
---|---|
status | +The status of the model | +
name: ModelStateEnum
+description: Status of a model
+from_schema: https://w3id.org/gocam
+rank: 1000
+permissible_values:
+ production:
+ text: production
+ development:
+ text: development
+
+
+
+An association between an activity and a molecular function term
+URI: gocam:MolecularFunctionAssociation
+Name | +Cardinality and Range | +Description | +Inheritance | +
---|---|---|---|
term | +0..1 MolecularFunctionTermObject |
+The ontology term that describes the nature of the association | +TermAssociation | +
type | +0..1 String |
++ | Association | +
evidence | +* EvidenceItem |
++ | Association | +
provenances | +* ProvenanceInfo |
++ | Association | +
used by | +used in | +type | +used | +
---|---|---|---|
Activity | +molecular_function | +range | +MolecularFunctionAssociation | +
Mapping Type | +Mapped Value | +
---|---|
self | +gocam:MolecularFunctionAssociation | +
native | +gocam:MolecularFunctionAssociation | +
name: MolecularFunctionAssociation
+description: An association between an activity and a molecular function term
+todos:
+- account for non-MF activity types in Reactome
+from_schema: https://w3id.org/gocam
+is_a: TermAssociation
+slot_usage:
+ term:
+ name: term
+ domain_of:
+ - EvidenceItem
+ - EnabledByAssociation
+ - TermAssociation
+ range: MolecularFunctionTermObject
+
+
+name: MolecularFunctionAssociation
+description: An association between an activity and a molecular function term
+todos:
+- account for non-MF activity types in Reactome
+from_schema: https://w3id.org/gocam
+is_a: TermAssociation
+slot_usage:
+ term:
+ name: term
+ domain_of:
+ - EvidenceItem
+ - EnabledByAssociation
+ - TermAssociation
+ range: MolecularFunctionTermObject
+attributes:
+ term:
+ name: term
+ description: The ontology term that describes the nature of the association
+ from_schema: https://w3id.org/gocam
+ alias: term
+ owner: MolecularFunctionAssociation
+ domain_of:
+ - EvidenceItem
+ - EnabledByAssociation
+ - TermAssociation
+ range: MolecularFunctionTermObject
+ type:
+ name: type
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ designates_type: true
+ alias: type
+ owner: MolecularFunctionAssociation
+ domain_of:
+ - Association
+ - Object
+ range: string
+ evidence:
+ name: evidence
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ multivalued: true
+ alias: evidence
+ owner: MolecularFunctionAssociation
+ domain_of:
+ - Association
+ range: EvidenceItem
+ inlined: true
+ provenances:
+ name: provenances
+ from_schema: https://w3id.org/gocam
+ multivalued: true
+ alias: provenances
+ owner: MolecularFunctionAssociation
+ domain_of:
+ - Model
+ - Activity
+ - EvidenceItem
+ - Association
+ range: ProvenanceInfo
+ inlined: true
+ inlined_as_list: true
+
+
+A term object that represents a molecular function term from GO
+URI: gocam:MolecularFunctionTermObject
+Name | +Cardinality and Range | +Description | +Inheritance | +
---|---|---|---|
id | +1 Uriorcurie |
++ | Object | +
label | +0..1 String |
++ | Object | +
type | +0..1 Uriorcurie |
++ | Object | +
obsolete | +0..1 Boolean |
++ | Object | +
used by | +used in | +type | +used | +
---|---|---|---|
MolecularFunctionAssociation | +term | +range | +MolecularFunctionTermObject | +
Instances of this class should have identifiers with one of the following prefixes:
+Mapping Type | +Mapped Value | +
---|---|
self | +gocam:MolecularFunctionTermObject | +
native | +gocam:MolecularFunctionTermObject | +
name: MolecularFunctionTermObject
+id_prefixes:
+- GO
+description: A term object that represents a molecular function term from GO
+from_schema: https://w3id.org/gocam
+is_a: TermObject
+
+
+name: MolecularFunctionTermObject
+id_prefixes:
+- GO
+description: A term object that represents a molecular function term from GO
+from_schema: https://w3id.org/gocam
+is_a: TermObject
+attributes:
+ id:
+ name: id
+ from_schema: https://w3id.org/gocam
+ identifier: true
+ alias: id
+ owner: MolecularFunctionTermObject
+ domain_of:
+ - Model
+ - Activity
+ - Object
+ range: uriorcurie
+ required: true
+ label:
+ name: label
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ slot_uri: rdfs:label
+ alias: label
+ owner: MolecularFunctionTermObject
+ domain_of:
+ - Object
+ range: string
+ type:
+ name: type
+ from_schema: https://w3id.org/gocam
+ designates_type: true
+ alias: type
+ owner: MolecularFunctionTermObject
+ domain_of:
+ - Association
+ - Object
+ range: uriorcurie
+ obsolete:
+ name: obsolete
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ alias: obsolete
+ owner: MolecularFunctionTermObject
+ domain_of:
+ - Object
+ range: boolean
+
+
+An association between an activity and a molecule term
+URI: gocam:MoleculeAssociation
+Name | +Cardinality and Range | +Description | +Inheritance | +
---|---|---|---|
term | +0..1 MoleculeTermObject |
+The ontology term that describes the nature of the association | +TermAssociation | +
type | +0..1 String |
++ | Association | +
evidence | +* EvidenceItem |
++ | Association | +
provenances | +* ProvenanceInfo |
++ | Association | +
used by | +used in | +type | +used | +
---|---|---|---|
Activity | +has_direct_input | +range | +MoleculeAssociation | +
Activity | +has_direct_output | +range | +MoleculeAssociation | +
Mapping Type | +Mapped Value | +
---|---|
self | +gocam:MoleculeAssociation | +
native | +gocam:MoleculeAssociation | +
name: MoleculeAssociation
+description: An association between an activity and a molecule term
+from_schema: https://w3id.org/gocam
+is_a: TermAssociation
+slot_usage:
+ term:
+ name: term
+ domain_of:
+ - EvidenceItem
+ - EnabledByAssociation
+ - TermAssociation
+ range: MoleculeTermObject
+
+
+name: MoleculeAssociation
+description: An association between an activity and a molecule term
+from_schema: https://w3id.org/gocam
+is_a: TermAssociation
+slot_usage:
+ term:
+ name: term
+ domain_of:
+ - EvidenceItem
+ - EnabledByAssociation
+ - TermAssociation
+ range: MoleculeTermObject
+attributes:
+ term:
+ name: term
+ description: The ontology term that describes the nature of the association
+ from_schema: https://w3id.org/gocam
+ alias: term
+ owner: MoleculeAssociation
+ domain_of:
+ - EvidenceItem
+ - EnabledByAssociation
+ - TermAssociation
+ range: MoleculeTermObject
+ type:
+ name: type
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ designates_type: true
+ alias: type
+ owner: MoleculeAssociation
+ domain_of:
+ - Association
+ - Object
+ range: string
+ evidence:
+ name: evidence
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ multivalued: true
+ alias: evidence
+ owner: MoleculeAssociation
+ domain_of:
+ - Association
+ range: EvidenceItem
+ inlined: true
+ provenances:
+ name: provenances
+ from_schema: https://w3id.org/gocam
+ multivalued: true
+ alias: provenances
+ owner: MoleculeAssociation
+ domain_of:
+ - Model
+ - Activity
+ - EvidenceItem
+ - Association
+ range: ProvenanceInfo
+ inlined: true
+ inlined_as_list: true
+
+
+A term object that represents a molecule term from CHEBI or UniProtKB
+ +Name | +Cardinality and Range | +Description | +Inheritance | +
---|---|---|---|
id | +1 Uriorcurie |
++ | Object | +
label | +0..1 String |
++ | Object | +
type | +0..1 Uriorcurie |
++ | Object | +
obsolete | +0..1 Boolean |
++ | Object | +
used by | +used in | +type | +used | +
---|---|---|---|
MoleculeAssociation | +term | +range | +MoleculeTermObject | +
Instances of this class should have identifiers with one of the following prefixes:
+CHEBI
+UniProtKB
+Mapping Type | +Mapped Value | +
---|---|
self | +gocam:MoleculeTermObject | +
native | +gocam:MoleculeTermObject | +
name: MoleculeTermObject
+id_prefixes:
+- CHEBI
+- UniProtKB
+description: A term object that represents a molecule term from CHEBI or UniProtKB
+from_schema: https://w3id.org/gocam
+is_a: TermObject
+
+
+name: MoleculeTermObject
+id_prefixes:
+- CHEBI
+- UniProtKB
+description: A term object that represents a molecule term from CHEBI or UniProtKB
+from_schema: https://w3id.org/gocam
+is_a: TermObject
+attributes:
+ id:
+ name: id
+ from_schema: https://w3id.org/gocam
+ identifier: true
+ alias: id
+ owner: MoleculeTermObject
+ domain_of:
+ - Model
+ - Activity
+ - Object
+ range: uriorcurie
+ required: true
+ label:
+ name: label
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ slot_uri: rdfs:label
+ alias: label
+ owner: MoleculeTermObject
+ domain_of:
+ - Object
+ range: string
+ type:
+ name: type
+ from_schema: https://w3id.org/gocam
+ designates_type: true
+ alias: type
+ owner: MoleculeTermObject
+ domain_of:
+ - Association
+ - Object
+ range: uriorcurie
+ obsolete:
+ name: obsolete
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ alias: obsolete
+ owner: MoleculeTermObject
+ domain_of:
+ - Object
+ range: boolean
+
+
+Prefix part of CURIE
+URI: xsd:string
+ +A URI, CURIE or BNODE that represents a node in a model.
+URI: shex:nonLiteral
+ +An abstract class for all identified objects in a model
+URI: gocam:Object
+Name | +Cardinality and Range | +Description | +Inheritance | +
---|---|---|---|
id | +1 Uriorcurie |
++ | direct | +
label | +0..1 String |
++ | direct | +
type | +0..1 Uriorcurie |
++ | direct | +
obsolete | +0..1 Boolean |
++ | direct | +
used by | +used in | +type | +used | +
---|---|---|---|
Model | +objects | +range | +Object | +
EvidenceItem | +with_objects | +range | +Object | +
Mapping Type | +Mapped Value | +
---|---|
self | +gocam:Object | +
native | +gocam:Object | +
name: Object
+description: An abstract class for all identified objects in a model
+from_schema: https://w3id.org/gocam
+attributes:
+ id:
+ name: id
+ from_schema: https://w3id.org/gocam
+ identifier: true
+ domain_of:
+ - Model
+ - Activity
+ - Object
+ range: uriorcurie
+ required: true
+ label:
+ name: label
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ slot_uri: rdfs:label
+ domain_of:
+ - Object
+ type:
+ name: type
+ from_schema: https://w3id.org/gocam
+ designates_type: true
+ domain_of:
+ - Association
+ - Object
+ range: uriorcurie
+ obsolete:
+ name: obsolete
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ domain_of:
+ - Object
+ range: boolean
+
+
+name: Object
+description: An abstract class for all identified objects in a model
+from_schema: https://w3id.org/gocam
+attributes:
+ id:
+ name: id
+ from_schema: https://w3id.org/gocam
+ identifier: true
+ alias: id
+ owner: Object
+ domain_of:
+ - Model
+ - Activity
+ - Object
+ range: uriorcurie
+ required: true
+ label:
+ name: label
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ slot_uri: rdfs:label
+ alias: label
+ owner: Object
+ domain_of:
+ - Object
+ range: string
+ type:
+ name: type
+ from_schema: https://w3id.org/gocam
+ designates_type: true
+ alias: type
+ owner: Object
+ domain_of:
+ - Association
+ - Object
+ range: uriorcurie
+ obsolete:
+ name: obsolete
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ alias: obsolete
+ owner: Object
+ domain_of:
+ - Object
+ range: boolean
+
+
+A term object that represents a phase term from GO or UBERON
+ +Name | +Cardinality and Range | +Description | +Inheritance | +
---|---|---|---|
id | +1 Uriorcurie |
++ | Object | +
label | +0..1 String |
++ | Object | +
type | +0..1 Uriorcurie |
++ | Object | +
obsolete | +0..1 Boolean |
++ | Object | +
Instances of this class should have identifiers with one of the following prefixes:
+GO
+UBERON
+PO
+Mapping Type | +Mapped Value | +
---|---|
self | +gocam:PhaseTermObject | +
native | +gocam:PhaseTermObject | +
name: PhaseTermObject
+id_prefixes:
+- GO
+- UBERON
+- PO
+description: A term object that represents a phase term from GO or UBERON
+from_schema: https://w3id.org/gocam
+is_a: TermObject
+
+
+name: PhaseTermObject
+id_prefixes:
+- GO
+- UBERON
+- PO
+description: A term object that represents a phase term from GO or UBERON
+from_schema: https://w3id.org/gocam
+is_a: TermObject
+attributes:
+ id:
+ name: id
+ from_schema: https://w3id.org/gocam
+ identifier: true
+ alias: id
+ owner: PhaseTermObject
+ domain_of:
+ - Model
+ - Activity
+ - Object
+ range: uriorcurie
+ required: true
+ label:
+ name: label
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ slot_uri: rdfs:label
+ alias: label
+ owner: PhaseTermObject
+ domain_of:
+ - Object
+ range: string
+ type:
+ name: type
+ from_schema: https://w3id.org/gocam
+ designates_type: true
+ alias: type
+ owner: PhaseTermObject
+ domain_of:
+ - Association
+ - Object
+ range: uriorcurie
+ obsolete:
+ name: obsolete
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ alias: obsolete
+ owner: PhaseTermObject
+ domain_of:
+ - Object
+ range: boolean
+
+
+A term object that represents a taxon term from NCBITaxon
+URI: gocam:PredicateTermObject
+Name | +Cardinality and Range | +Description | +Inheritance | +
---|---|---|---|
id | +1 Uriorcurie |
++ | Object | +
label | +0..1 String |
++ | Object | +
type | +0..1 Uriorcurie |
++ | Object | +
obsolete | +0..1 Boolean |
++ | Object | +
used by | +used in | +type | +used | +
---|---|---|---|
CausalAssociation | +predicate | +range | +PredicateTermObject | +
Instances of this class should have identifiers with one of the following prefixes:
+Mapping Type | +Mapped Value | +
---|---|
self | +gocam:PredicateTermObject | +
native | +gocam:PredicateTermObject | +
name: PredicateTermObject
+id_prefixes:
+- RO
+description: A term object that represents a taxon term from NCBITaxon
+from_schema: https://w3id.org/gocam
+is_a: TermObject
+
+
+name: PredicateTermObject
+id_prefixes:
+- RO
+description: A term object that represents a taxon term from NCBITaxon
+from_schema: https://w3id.org/gocam
+is_a: TermObject
+attributes:
+ id:
+ name: id
+ from_schema: https://w3id.org/gocam
+ identifier: true
+ alias: id
+ owner: PredicateTermObject
+ domain_of:
+ - Model
+ - Activity
+ - Object
+ range: uriorcurie
+ required: true
+ label:
+ name: label
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ slot_uri: rdfs:label
+ alias: label
+ owner: PredicateTermObject
+ domain_of:
+ - Object
+ range: string
+ type:
+ name: type
+ from_schema: https://w3id.org/gocam
+ designates_type: true
+ alias: type
+ owner: PredicateTermObject
+ domain_of:
+ - Association
+ - Object
+ range: uriorcurie
+ obsolete:
+ name: obsolete
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ alias: obsolete
+ owner: PredicateTermObject
+ domain_of:
+ - Object
+ range: boolean
+
+
+A term object that represents a protein complex term from GO
+URI: gocam:ProteinComplexTermObject
+Name | +Cardinality and Range | +Description | +Inheritance | +
---|---|---|---|
id | +1 Uriorcurie |
++ | Object | +
label | +0..1 String |
++ | Object | +
type | +0..1 Uriorcurie |
++ | Object | +
obsolete | +0..1 Boolean |
++ | Object | +
used by | +used in | +type | +used | +
---|---|---|---|
EnabledByProteinComplexAssociation | +term | +range | +ProteinComplexTermObject | +
Mapping Type | +Mapped Value | +
---|---|
self | +gocam:ProteinComplexTermObject | +
native | +gocam:ProteinComplexTermObject | +
name: ProteinComplexTermObject
+description: A term object that represents a protein complex term from GO
+from_schema: https://w3id.org/gocam
+is_a: InformationBiomacromoleculeTermObject
+
+
+name: ProteinComplexTermObject
+description: A term object that represents a protein complex term from GO
+from_schema: https://w3id.org/gocam
+is_a: InformationBiomacromoleculeTermObject
+attributes:
+ id:
+ name: id
+ from_schema: https://w3id.org/gocam
+ identifier: true
+ alias: id
+ owner: ProteinComplexTermObject
+ domain_of:
+ - Model
+ - Activity
+ - Object
+ range: uriorcurie
+ required: true
+ label:
+ name: label
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ slot_uri: rdfs:label
+ alias: label
+ owner: ProteinComplexTermObject
+ domain_of:
+ - Object
+ range: string
+ type:
+ name: type
+ from_schema: https://w3id.org/gocam
+ designates_type: true
+ alias: type
+ owner: ProteinComplexTermObject
+ domain_of:
+ - Association
+ - Object
+ range: uriorcurie
+ obsolete:
+ name: obsolete
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ alias: obsolete
+ owner: ProteinComplexTermObject
+ domain_of:
+ - Object
+ range: boolean
+
+
+Provenance information for an object
+URI: gocam:ProvenanceInfo
+Name | +Cardinality and Range | +Description | +Inheritance | +
---|---|---|---|
contributor | +0..1 String |
++ | direct | +
created | +0..1 String |
++ | direct | +
date | +0..1 String |
++ | direct | +
provided_by | +0..1 String |
++ | direct | +
used by | +used in | +type | +used | +
---|---|---|---|
Model | +provenances | +range | +ProvenanceInfo | +
Activity | +provenances | +range | +ProvenanceInfo | +
EvidenceItem | +provenances | +range | +ProvenanceInfo | +
Association | +provenances | +range | +ProvenanceInfo | +
EnabledByAssociation | +provenances | +range | +ProvenanceInfo | +
EnabledByGeneProductAssociation | +provenances | +range | +ProvenanceInfo | +
EnabledByProteinComplexAssociation | +provenances | +range | +ProvenanceInfo | +
CausalAssociation | +provenances | +range | +ProvenanceInfo | +
TermAssociation | +provenances | +range | +ProvenanceInfo | +
MolecularFunctionAssociation | +provenances | +range | +ProvenanceInfo | +
BiologicalProcessAssociation | +provenances | +range | +ProvenanceInfo | +
CellularAnatomicalEntityAssociation | +provenances | +range | +ProvenanceInfo | +
CellTypeAssociation | +provenances | +range | +ProvenanceInfo | +
GrossAnatomyAssociation | +provenances | +range | +ProvenanceInfo | +
MoleculeAssociation | +provenances | +range | +ProvenanceInfo | +
Mapping Type | +Mapped Value | +
---|---|
self | +gocam:ProvenanceInfo | +
native | +gocam:ProvenanceInfo | +
name: ProvenanceInfo
+description: Provenance information for an object
+from_schema: https://w3id.org/gocam
+attributes:
+ contributor:
+ name: contributor
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ slot_uri: dct:contributor
+ domain_of:
+ - ProvenanceInfo
+ created:
+ name: created
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ slot_uri: dct:created
+ domain_of:
+ - ProvenanceInfo
+ date:
+ name: date
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ slot_uri: dct:date
+ domain_of:
+ - ProvenanceInfo
+ provided_by:
+ name: provided_by
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ slot_uri: pav:providedBy
+ domain_of:
+ - ProvenanceInfo
+
+
+name: ProvenanceInfo
+description: Provenance information for an object
+from_schema: https://w3id.org/gocam
+attributes:
+ contributor:
+ name: contributor
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ slot_uri: dct:contributor
+ alias: contributor
+ owner: ProvenanceInfo
+ domain_of:
+ - ProvenanceInfo
+ range: string
+ created:
+ name: created
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ slot_uri: dct:created
+ alias: created
+ owner: ProvenanceInfo
+ domain_of:
+ - ProvenanceInfo
+ range: string
+ date:
+ name: date
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ slot_uri: dct:date
+ alias: date
+ owner: ProvenanceInfo
+ domain_of:
+ - ProvenanceInfo
+ range: string
+ provided_by:
+ name: provided_by
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ slot_uri: pav:providedBy
+ alias: provided_by
+ owner: ProvenanceInfo
+ domain_of:
+ - ProvenanceInfo
+ range: string
+
+
+An object that represents a publication or other kind of reference
+ +Name | +Cardinality and Range | +Description | +Inheritance | +
---|---|---|---|
abstract_text | +0..1 String |
++ | direct | +
full_text | +0..1 String |
++ | direct | +
id | +1 Uriorcurie |
++ | Object | +
label | +0..1 String |
++ | Object | +
type | +0..1 Uriorcurie |
++ | Object | +
obsolete | +0..1 Boolean |
++ | Object | +
used by | +used in | +type | +used | +
---|---|---|---|
EvidenceItem | +reference | +range | +PublicationObject | +
Instances of this class should have identifiers with one of the following prefixes:
+PMID
+GOREF
+DOI
+Mapping Type | +Mapped Value | +
---|---|
self | +gocam:PublicationObject | +
native | +gocam:PublicationObject | +
name: PublicationObject
+id_prefixes:
+- PMID
+- GOREF
+- DOI
+description: An object that represents a publication or other kind of reference
+from_schema: https://w3id.org/gocam
+is_a: Object
+attributes:
+ abstract_text:
+ name: abstract_text
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ domain_of:
+ - PublicationObject
+ full_text:
+ name: full_text
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ domain_of:
+ - PublicationObject
+
+
+name: PublicationObject
+id_prefixes:
+- PMID
+- GOREF
+- DOI
+description: An object that represents a publication or other kind of reference
+from_schema: https://w3id.org/gocam
+is_a: Object
+attributes:
+ abstract_text:
+ name: abstract_text
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ alias: abstract_text
+ owner: PublicationObject
+ domain_of:
+ - PublicationObject
+ range: string
+ full_text:
+ name: full_text
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ alias: full_text
+ owner: PublicationObject
+ domain_of:
+ - PublicationObject
+ range: string
+ id:
+ name: id
+ from_schema: https://w3id.org/gocam
+ identifier: true
+ alias: id
+ owner: PublicationObject
+ domain_of:
+ - Model
+ - Activity
+ - Object
+ range: uriorcurie
+ required: true
+ label:
+ name: label
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ slot_uri: rdfs:label
+ alias: label
+ owner: PublicationObject
+ domain_of:
+ - Object
+ range: string
+ type:
+ name: type
+ from_schema: https://w3id.org/gocam
+ designates_type: true
+ alias: type
+ owner: PublicationObject
+ domain_of:
+ - Association
+ - Object
+ range: uriorcurie
+ obsolete:
+ name: obsolete
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ alias: obsolete
+ owner: PublicationObject
+ domain_of:
+ - Object
+ range: boolean
+
+
+A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.
+URI: xsd:string
+ +A character string
+URI: xsd:string
+ +A term object that represents a taxon term from NCBITaxon
+ +Name | +Cardinality and Range | +Description | +Inheritance | +
---|---|---|---|
id | +1 Uriorcurie |
++ | Object | +
label | +0..1 String |
++ | Object | +
type | +0..1 Uriorcurie |
++ | Object | +
obsolete | +0..1 Boolean |
++ | Object | +
used by | +used in | +type | +used | +
---|---|---|---|
Model | +taxon | +range | +TaxonTermObject | +
Instances of this class should have identifiers with one of the following prefixes:
+Mapping Type | +Mapped Value | +
---|---|
self | +gocam:TaxonTermObject | +
native | +gocam:TaxonTermObject | +
name: TaxonTermObject
+id_prefixes:
+- NCBITaxon
+description: A term object that represents a taxon term from NCBITaxon
+from_schema: https://w3id.org/gocam
+is_a: TermObject
+
+
+name: TaxonTermObject
+id_prefixes:
+- NCBITaxon
+description: A term object that represents a taxon term from NCBITaxon
+from_schema: https://w3id.org/gocam
+is_a: TermObject
+attributes:
+ id:
+ name: id
+ from_schema: https://w3id.org/gocam
+ identifier: true
+ alias: id
+ owner: TaxonTermObject
+ domain_of:
+ - Model
+ - Activity
+ - Object
+ range: uriorcurie
+ required: true
+ label:
+ name: label
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ slot_uri: rdfs:label
+ alias: label
+ owner: TaxonTermObject
+ domain_of:
+ - Object
+ range: string
+ type:
+ name: type
+ from_schema: https://w3id.org/gocam
+ designates_type: true
+ alias: type
+ owner: TaxonTermObject
+ domain_of:
+ - Association
+ - Object
+ range: uriorcurie
+ obsolete:
+ name: obsolete
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ alias: obsolete
+ owner: TaxonTermObject
+ domain_of:
+ - Object
+ range: boolean
+
+
+An association between an activity and a term, potentially with extensions
+Name | +Cardinality and Range | +Description | +Inheritance | +
---|---|---|---|
term | +0..1 TermObject |
+The ontology term that describes the nature of the association | +direct | +
type | +0..1 String |
++ | Association | +
evidence | +* EvidenceItem |
++ | Association | +
provenances | +* ProvenanceInfo |
++ | Association | +
Mapping Type | +Mapped Value | +
---|---|
self | +gocam:TermAssociation | +
native | +gocam:TermAssociation | +
name: TermAssociation
+description: An association between an activity and a term, potentially with extensions
+from_schema: https://w3id.org/gocam
+is_a: Association
+abstract: true
+attributes:
+ term:
+ name: term
+ description: The ontology term that describes the nature of the association
+ from_schema: https://w3id.org/gocam
+ domain_of:
+ - EvidenceItem
+ - EnabledByAssociation
+ - TermAssociation
+ range: TermObject
+
+
+name: TermAssociation
+description: An association between an activity and a term, potentially with extensions
+from_schema: https://w3id.org/gocam
+is_a: Association
+abstract: true
+attributes:
+ term:
+ name: term
+ description: The ontology term that describes the nature of the association
+ from_schema: https://w3id.org/gocam
+ alias: term
+ owner: TermAssociation
+ domain_of:
+ - EvidenceItem
+ - EnabledByAssociation
+ - TermAssociation
+ range: TermObject
+ type:
+ name: type
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ designates_type: true
+ alias: type
+ owner: TermAssociation
+ domain_of:
+ - Association
+ - Object
+ range: string
+ evidence:
+ name: evidence
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ multivalued: true
+ alias: evidence
+ owner: TermAssociation
+ domain_of:
+ - Association
+ range: EvidenceItem
+ inlined: true
+ provenances:
+ name: provenances
+ from_schema: https://w3id.org/gocam
+ multivalued: true
+ alias: provenances
+ owner: TermAssociation
+ domain_of:
+ - Model
+ - Activity
+ - EvidenceItem
+ - Association
+ range: ProvenanceInfo
+ inlined: true
+ inlined_as_list: true
+
+
+An abstract class for all ontology term objects
+URI: gocam:TermObject
+Name | +Cardinality and Range | +Description | +Inheritance | +
---|---|---|---|
id | +1 Uriorcurie |
++ | Object | +
label | +0..1 String |
++ | Object | +
type | +0..1 Uriorcurie |
++ | Object | +
obsolete | +0..1 Boolean |
++ | Object | +
used by | +used in | +type | +used | +
---|---|---|---|
TermAssociation | +term | +range | +TermObject | +
Mapping Type | +Mapped Value | +
---|---|
self | +gocam:TermObject | +
native | +gocam:TermObject | +
name: TermObject
+description: An abstract class for all ontology term objects
+from_schema: https://w3id.org/gocam
+is_a: Object
+abstract: true
+
+
+name: TermObject
+description: An abstract class for all ontology term objects
+from_schema: https://w3id.org/gocam
+is_a: Object
+abstract: true
+attributes:
+ id:
+ name: id
+ from_schema: https://w3id.org/gocam
+ identifier: true
+ alias: id
+ owner: TermObject
+ domain_of:
+ - Model
+ - Activity
+ - Object
+ range: uriorcurie
+ required: true
+ label:
+ name: label
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ slot_uri: rdfs:label
+ alias: label
+ owner: TermObject
+ domain_of:
+ - Object
+ range: string
+ type:
+ name: type
+ from_schema: https://w3id.org/gocam
+ designates_type: true
+ alias: type
+ owner: TermObject
+ domain_of:
+ - Association
+ - Object
+ range: uriorcurie
+ obsolete:
+ name: obsolete
+ from_schema: https://w3id.org/gocam
+ rank: 1000
+ alias: obsolete
+ owner: TermObject
+ domain_of:
+ - Object
+ range: boolean
+
+
+a complete URI
+URI: xsd:anyURI
+ +a URI or a CURIE
+URI: xsd:anyURI
+ +GO CAM Data Model (Python)
+ + + + + + +URI: gocam:abstract_text
+ + +Name | +Description | +Modifies Slot | +
---|---|---|
PublicationObject | +An object that represents a publication or other kind of reference | +no | +
name: abstract_text
+from_schema: https://w3id.org/gocam
+rank: 1000
+alias: abstract_text
+owner: PublicationObject
+domain_of:
+- PublicationObject
+range: string
+
+
+
+All of the activities that are part of the model
+URI: gocam:activities
+ + +Name | +Description | +Modifies Slot | +
---|---|---|
Model | +A model of a biological program consisting of a set of causally connected act... | +no | +
Range: Activity
+Multivalued: True
+name: activities
+description: All of the activities that are part of the model
+from_schema: https://w3id.org/gocam
+rank: 1000
+multivalued: true
+alias: activities
+owner: Model
+domain_of:
+- Model
+range: Activity
+inlined: true
+inlined_as_list: true
+
+
+
+\n {translation(\"search.result.term.missing\")}: {...missing}\n
\n }\n