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 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 |
|---|---|
| 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 | |
| date_modified | The date that the model was last modified |
| 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 | A generic slot for part-of relationships |
| predicate | The RO relation that represents the type of relationship |
| provenances | A generic slot for 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 |
| taxon_label | The label of the primary taxon for the model |
| term | A generic slot for ontology terms |
| 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 |
|---|---|