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
Activity	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
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 potential gene products
that carry out that activity.
EnabledByGeneProductAssociation	An association between an activity and an individual gene product
EnabledByProteinComplexAssociation	An association between an activity and a protein complex, where the complex carries out the activity. This should only be used when the activity cannot be attributed to an individual member of the complex, but instead the function is an emergent property of the complex.
TermAssociation	An association between an activity and a term, potentially with extensions. This is an abstract class for grouping purposes, it should not be directly instantiated, instead a subclass should be instantiated.
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 model
Model	A model of a biological program consisting of a set of causally connected activities.
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. Only ECO terms that map up to a GO GAF evidence code should be used.
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 query or index operations. Note that this index is not typically populated in the working transactional store for a model, it is derived via computation from core primary model information.

Slots

Slot	Description
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
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
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_has_input_closure
model_activity_has_input_terms
model_activity_molecular_function_closure	The reflexive transitive closure of model_activity_molecular_function_terms...
model_activity_molecular_function_terms	All MF terms for all activities
model_activity_occurs_in_closure
model_activity_occurs_in_terms
model_activity_part_of_closure
model_activity_part_of_terms
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
start_activities
status	The status of the model in terms of its progression along the developmental l...
taxon	The primary taxon that the model is about
taxon_closure
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
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