gocam
Gene Ontology Causal Activity Model (GO-CAM) Schema.
This schema provides a way of representing causal pathway Models. A model consists of a set of Activity objects, where each activity object represents the function of either an individual gene product, a protein complex of gene products, or a set of possible gene products.
Each Models has associated metadata slots. Some slots such as id, title, and status are required.
URI: https://w3id.org/gocam
Name: gocam
Classes
Class | Description |
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Activity | An individual activity in a causal model, representing the individual molecul... |
Association | An abstract grouping for different kinds of evidence-associated provenance |
CausalAssociation | A causal association between two activities |
EnabledByAssociation | An association between an activity and the gene product or complex or set of ... |
EnabledByGeneProductAssociation | An association between an activity and an individual gene product |
EnabledByProteinComplexAssociation | An association between an activity and a protein complex, where the complex c... |
TermAssociation | An association between an activity and a term, potentially with extensions |
BiologicalProcessAssociation | An association between an activity and a biological process term |
CellTypeAssociation | An association between an activity and a cell type term |
CellularAnatomicalEntityAssociation | An association between an activity and a cellular anatomical entity term |
GrossAnatomyAssociation | An association between an activity and a gross anatomical structure term |
MolecularFunctionAssociation | An association between an activity and a molecular function term |
MoleculeAssociation | An association between an activity and a molecule term |
EvidenceItem | An individual piece of evidence that is associated with an assertion in a mod... |
Model | A model of a biological program consisting of a set of causally connected act... |
Object | An abstract class for all identified objects in a model |
PublicationObject | An object that represents a publication or other kind of reference |
TermObject | An abstract class for all ontology term objects |
BiologicalProcessTermObject | A term object that represents a biological process term from GO |
CellTypeTermObject | A term object that represents a cell type term from CL |
CellularAnatomicalEntityTermObject | A term object that represents a cellular anatomical entity term from GO |
EvidenceTermObject | A term object that represents an evidence term from ECO |
GrossAnatomicalStructureTermObject | A term object that represents a gross anatomical structure term from UBERON |
InformationBiomacromoleculeTermObject | An abstract class for all information biomacromolecule term objects |
GeneProductTermObject | A term object that represents a gene product term from GO or UniProtKB |
ProteinComplexTermObject | A term object that represents a protein complex term from GO |
MolecularFunctionTermObject | A term object that represents a molecular function term from GO |
MoleculeTermObject | A term object that represents a molecule term from CHEBI or UniProtKB |
PhaseTermObject | A term object that represents a phase term from GO or UBERON |
PredicateTermObject | A term object that represents a taxon term from NCBITaxon |
TaxonTermObject | A term object that represents a taxon term from NCBITaxon |
ProvenanceInfo | Provenance information for an object |
QueryIndex | An index that is optionally placed on a model in order to support common quer... |
Slots
Slot | Description |
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abstract_text | |
activities | All of the activities that are part of the model |
additional_taxa | Additional taxa that the model is about |
annoton_terms | |
causal_associations | The causal associations that flow out of this activity |
comments | Curator-provided comments about the model |
contributor | |
created | |
date | |
downstream_activity | The activity unit that is downstream of this one |
enabled_by | The gene product or complex that carries out the activity |
end_activities | The set of activities that are the end points of the model, i |
evidence | The set of evidence items that support the association |
flattened_references | All publication objects from the model across different levels combined in on... |
full_text | |
happens_during | Optional extension describing where the BP takes place |
has_input | The input molecules that are directly consumed by the activity |
has_output | The output molecules that are directly produced by the activity |
has_primary_input | The primary input molecule that is directly consumed by the activity |
has_primary_output | The primary output molecule that is directly produced by the activity |
id | The identifier of the model |
intermediate_activities | The set of activities that are neither start nor end activities, i |
label | |
length_of_longest_causal_association_path | The maximum number of hops along activities along the direction of causal flo... |
members | The gene products that are part of the complex |
model_activity_enabled_by_closure | The reflexive transitive closure of model_activity_enabled_by_terms , over t... |
model_activity_enabled_by_rollup | The rollup of model_activity_enabled_by_closure to a GO subset or slim |
model_activity_enabled_by_terms | All direct enabler terms for all activities |
model_activity_has_input_closure | The reflexive transitive closure of model_activity_has_input_terms , over th... |
model_activity_has_input_rollup | The rollup of model_activity_has_input_closure to a GO subset or slim |
model_activity_has_input_terms | All direct input terms for all activities |
model_activity_molecular_function_closure | The reflexive transitive closure of model_activity_molecular_function_terms ... |
model_activity_molecular_function_rollup | The rollup of model_activity_molecular_function_closure to a GO subset or s... |
model_activity_molecular_function_terms | All MF terms for all activities |
model_activity_occurs_in_closure | The reflexive transitive closure of model_activity_occurs_in_terms , over th... |
model_activity_occurs_in_rollup | The rollup of model_activity_occurs_in_closure to a GO subset or slim |
model_activity_occurs_in_terms | All direct cellular component localization terms for all activities |
model_activity_part_of_closure | The reflexive transitive closure of model_activity_part_of_terms , over the ... |
model_activity_part_of_rollup | The rollup of model_activity_part_of_closure to a GO subset or slim |
model_activity_part_of_terms | All direct biological process terms for all activities |
model_taxon | The primary taxon term for the model, over the NCBITaxon:subClassOf relations... |
model_taxon_closure | The reflexive transitive closure of the taxon term for the model, over the NC... |
model_taxon_rollup | The rollup of the taxon closure to a NCBITaxon subset or slim |
molecular_function | The molecular function that is carried out by the gene product or complex |
number_of_activities | The number of activities in a model |
number_of_causal_associations | Total number of causal association edges connecting activities in a model |
number_of_enabled_by_terms | The number of molecular entities or sets of entities in a model |
number_of_end_activities | The number of end activities in a model |
number_of_intermediate_activities | The number of intermediate activities in a model |
number_of_singleton_activities | The number of singleton activities in a model |
number_of_start_activities | The number of start activities in a model |
number_of_strongly_connected_components | The number of distinct components that consist of activities that are connect... |
objects | All of the objects that are part of the model |
obsolete | |
occurs_in | The cellular location in which the activity occurs |
part_of | The larger biological process in which the activity is a part |
predicate | The RO relation that represents the type of relationship |
provenances | Model-level provenance information |
provided_by | |
query_index | An optional object that contains the results of indexing a model with various... |
reference | The publication of reference that describes the evidence |
singleton_activities | The set of activities that have no causal associations, i |
start_activities | The set of activities that are the starting points of the model, i |
status | The status of the model in terms of its progression along the developmental l... |
taxon | The primary taxon that the model is about |
term | The ECO term representing the type of evidence |
title | The human-readable descriptive title of the model |
type | The type of association |
with_objects | Supporting database entities or terms |
Enumerations
Enumeration | Description |
---|---|
CausalPredicateEnum | A term describing the causal relationship between two activities |
CellularAnatomicalEntityEnum | A term from the subset of the cellular anatomical entity branch of GO CC |
EvidenceCodeEnum | A term from the subset of ECO that maps up to a GAF evidence code |
InformationBiomacromoleculeCategory | A term describing the type of the enabler of an activity |
ModelStateEnum | A term describing where the model is in the development life cycle |
PhaseEnum | A term from either the phase branch of GO or the phase branch of an anatomy o... |
Types
Type | Description |
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Boolean | A binary (true or false) value |
Curie | a compact URI |
Date | a date (year, month and day) in an idealized calendar |
DateOrDatetime | Either a date or a datetime |
Datetime | The combination of a date and time |
Decimal | A real number with arbitrary precision that conforms to the xsd:decimal speci... |
Double | A real number that conforms to the xsd:double specification |
Float | A real number that conforms to the xsd:float specification |
Integer | An integer |
Jsonpath | A string encoding a JSON Path |
Jsonpointer | A string encoding a JSON Pointer |
Ncname | Prefix part of CURIE |
Nodeidentifier | A URI, CURIE or BNODE that represents a node in a model |
Objectidentifier | A URI or CURIE that represents an object in the model |
Sparqlpath | A string encoding a SPARQL Property Path |
String | A character string |
Time | A time object represents a (local) time of day, independent of any particular... |
Uri | a complete URI |
Uriorcurie | a URI or a CURIE |
Subsets
Subset | Description |
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