Class: SequenceEntity

name: sequence_entity
description: Sequence-bearing physical entity linked to a stable reference sequence
  and optionally decorated with residue modifications and subsequence coordinates.
comments:
- Core Reactome pattern for proteins, RNAs, and other accessioned biomolecules in
  specific states.
from_schema: https://w3id.org/reactome-ontology
is_a: genome_encoded_entity
slots:
- has_reference_entity
- has_modified_residue
- start_coordinate
- end_coordinate
- sequence_reference_type
slot_usage:
  has_reference_entity:
    name: has_reference_entity
    range: reference_sequence
    required: true
class_uri: reactome:SequenceEntity

name: sequence_entity
description: Sequence-bearing physical entity linked to a stable reference sequence
  and optionally decorated with residue modifications and subsequence coordinates.
comments:
- Core Reactome pattern for proteins, RNAs, and other accessioned biomolecules in
  specific states.
from_schema: https://w3id.org/reactome-ontology
is_a: genome_encoded_entity
slot_usage:
  has_reference_entity:
    name: has_reference_entity
    range: reference_sequence
    required: true
attributes:
  has_reference_entity:
    name: has_reference_entity
    description: Invariant reference identity underlying a contextualized physical
      entity.
    comments:
    - '{''One of the key distinctions in Reactome'': ''reference identity is separate
      from stateful physical instantiation.''}'
    from_schema: https://w3id.org/reactome-ontology
    rank: 1000
    slot_uri: reactome:hasReferenceEntity
    alias: has_reference_entity
    owner: sequence_entity
    domain_of:
    - simple_entity
    - sequence_entity
    range: reference_sequence
    required: true
    multivalued: false
  has_modified_residue:
    name: has_modified_residue
    description: Modified residue feature borne by a sequence-based physical entity.
    comments:
    - Supports phosphorylation, cleavage, ubiquitination, and related residue-level
      state modeling.
    from_schema: https://w3id.org/reactome-ontology
    rank: 1000
    slot_uri: reactome:hasModifiedResidue
    alias: has_modified_residue
    owner: sequence_entity
    domain_of:
    - sequence_entity
    range: abstract_modified_residue
    multivalued: true
    inlined: true
    inlined_as_list: true
  start_coordinate:
    name: start_coordinate
    description: Start coordinate of a subsequence, fragment, or feature-bearing region
      on a sequence entity.
    comments:
    - Useful for proteolytic fragments, domains, and sequence-trimmed entity forms.
    from_schema: https://w3id.org/reactome-ontology
    rank: 1000
    slot_uri: reactome:startCoordinate
    alias: start_coordinate
    owner: sequence_entity
    domain_of:
    - sequence_entity
    range: integer
    multivalued: false
  end_coordinate:
    name: end_coordinate
    description: End coordinate of a subsequence, fragment, or feature-bearing region
      on a sequence entity.
    comments:
    - Typically paired with start_coordinate.
    from_schema: https://w3id.org/reactome-ontology
    rank: 1000
    slot_uri: reactome:endCoordinate
    alias: end_coordinate
    owner: sequence_entity
    domain_of:
    - sequence_entity
    range: integer
    multivalued: false
  sequence_reference_type:
    name: sequence_reference_type
    description: Textual qualifier for the kind of referenced sequence or entity.
    comments:
    - Included for compatibility with Reactome exports.
    from_schema: https://w3id.org/reactome-ontology
    rank: 1000
    slot_uri: reactome:sequenceReferenceType
    alias: sequence_reference_type
    owner: sequence_entity
    domain_of:
    - sequence_entity
    range: string
    multivalued: false
  in_taxon:
    name: in_taxon
    description: Taxon in which the object, event, or entity is asserted to occur
      or be defined.
    comments:
    - For events this denotes the organism context; for entities it denotes the biological
      source organism.
    from_schema: https://w3id.org/reactome-ontology
    rank: 1000
    slot_uri: reactome:inTaxon
    alias: in_taxon
    owner: sequence_entity
    domain_of:
    - event
    - physical_entity
    range: organism_taxon
    multivalued: true
  located_in_compartment:
    name: located_in_compartment
    description: Compartment in which an entity resides or an event occurs.
    comments:
    - In Reactome, compartment is identity-relevant for many physical entities.
    from_schema: https://w3id.org/reactome-ontology
    rank: 1000
    slot_uri: reactome:locatedInCompartment
    alias: located_in_compartment
    owner: sequence_entity
    domain_of:
    - event
    - physical_entity
    range: compartment
    multivalued: true
  has_cross_reference:
    name: has_cross_reference
    description: External cross-reference to another database or controlled resource.
    comments:
    - Used for interoperating with identifiers from GO, ChEBI, UniProt, Ensembl, and
      related resources.
    from_schema: https://w3id.org/reactome-ontology
    rank: 1000
    slot_uri: reactome:hasCrossReference
    alias: has_cross_reference
    owner: sequence_entity
    domain_of:
    - event
    - physical_entity
    range: database_identifier
    multivalued: true
  has_disease_context:
    name: has_disease_context
    description: Disease context associated with an event or physical entity.
    comments:
    - Represents contextual disease association rather than broad etiologic modeling.
    from_schema: https://w3id.org/reactome-ontology
    rank: 1000
    slot_uri: reactome:hasDiseaseContext
    alias: has_disease_context
    owner: sequence_entity
    domain_of:
    - event
    - physical_entity
    range: disease
    multivalued: true
  has_go_cellular_component:
    name: has_go_cellular_component
    description: GO cellular component term associated with a physical entity or event
      context.
    comments:
    - Often complements the explicit compartment modeling in Reactome.
    from_schema: https://w3id.org/reactome-ontology
    rank: 1000
    slot_uri: reactome:hasGoCellularComponent
    alias: has_go_cellular_component
    owner: sequence_entity
    domain_of:
    - physical_entity
    range: go_cellular_component_term
    multivalued: false
  systematic_name:
    name: systematic_name
    description: Formal or systematic name for an entity when available.
    comments:
    - Often useful for chemicals, complexes, or sequence-derived entities.
    from_schema: https://w3id.org/reactome-ontology
    rank: 1000
    slot_uri: reactome:systematicName
    alias: systematic_name
    owner: sequence_entity
    domain_of:
    - physical_entity
    range: string
    multivalued: false
  is_in_disease_context:
    name: is_in_disease_context
    description: Boolean flag indicating that the represented entity is contextualized
      to a disease state.
    comments:
    - This is a contextual flag and does not by itself define a disease ontology class.
    from_schema: https://w3id.org/reactome-ontology
    rank: 1000
    slot_uri: reactome:isInDiseaseContext
    alias: is_in_disease_context
    owner: sequence_entity
    domain_of:
    - physical_entity
    range: boolean
    multivalued: false
  reactome_db_id:
    name: reactome_db_id
    description: Internal Reactome database identifier assigned to a database object.
    comments:
    - Reactome DB_ID values are implementation-oriented identifiers rather than stable
      public identifiers.
    from_schema: https://w3id.org/reactome-ontology
    rank: 1000
    slot_uri: reactome:reactomeDbId
    alias: reactome_db_id
    owner: sequence_entity
    domain_of:
    - database_object
    range: integer
    required: true
    multivalued: false
  reactome_stable_identifier:
    name: reactome_stable_identifier
    description: Stable public Reactome identifier for an object.
    comments:
    - Typically corresponds to the curated Reactome stable accession such as R-HSA-xxxxx.
    from_schema: https://w3id.org/reactome-ontology
    rank: 1000
    slot_uri: reactome:reactomeStableIdentifier
    alias: reactome_stable_identifier
    owner: sequence_entity
    domain_of:
    - database_object
    range: string
    required: true
    multivalued: false
  source_schema_class:
    name: source_schema_class
    description: Name of the source Reactome schema class from which the instance
      derives.
    comments:
    - Useful when preserving frame-schema provenance or round-tripping with the original
      Reactome graph.
    from_schema: https://w3id.org/reactome-ontology
    rank: 1000
    slot_uri: reactome:sourceSchemaClass
    alias: source_schema_class
    owner: sequence_entity
    domain_of:
    - database_object
    range: string
    required: true
    multivalued: false
  display_label:
    name: display_label
    description: Preferred display label used by Reactome for user-facing presentation.
    comments:
    - Often combines identity and contextual state into a concise label.
    from_schema: https://w3id.org/reactome-ontology
    rank: 1000
    is_a: name
    slot_uri: reactome:displayLabel
    alias: display_label
    owner: sequence_entity
    domain_of:
    - database_object
    range: string
    required: true
    multivalued: false
  definition:
    name: definition
    description: Curated textual definition that states what the object is.
    comments:
    - Intended for conceptual definitions rather than narrative summaries.
    from_schema: https://w3id.org/reactome-ontology
    rank: 1000
    slot_uri: reactome:definition
    alias: definition
    owner: sequence_entity
    domain_of:
    - database_object
    range: string
    multivalued: false
  previous_stable_identifier:
    name: previous_stable_identifier
    description: Deprecated or previous stable Reactome identifier retained for traceability.
    comments:
    - Useful during migration, identifier replacement, and legacy resolution.
    from_schema: https://w3id.org/reactome-ontology
    rank: 1000
    slot_uri: reactome:previousStableIdentifier
    alias: previous_stable_identifier
    owner: sequence_entity
    domain_of:
    - database_object
    range: string
    multivalued: false
  created:
    name: created
    description: Provenance link to the curation event that originally created the
      object record.
    comments:
    - Usually points to an InstanceEdit containing editor and date metadata.
    from_schema: https://w3id.org/reactome-ontology
    rank: 1000
    slot_uri: reactome:created
    alias: created
    owner: sequence_entity
    domain_of:
    - database_object
    range: instance_edit
    required: true
    multivalued: false
  modified:
    name: modified
    description: Provenance links to subsequent modifications of the object record.
    comments:
    - Multiple modifications are common across curation history.
    from_schema: https://w3id.org/reactome-ontology
    rank: 1000
    slot_uri: reactome:modified
    alias: modified
    owner: sequence_entity
    domain_of:
    - database_object
    range: instance_edit
    multivalued: true
  id:
    name: id
    description: Unique identifier for an instance in the serialized dataset.
    comments:
    - This may be a local identifier, CURIE, URI, or other serialization key.
    from_schema: https://w3id.org/reactome-ontology
    rank: 1000
    slot_uri: dcterms:identifier
    identifier: true
    alias: id
    owner: sequence_entity
    domain_of:
    - named_entity
    range: string
    required: true
  name:
    name: name
    description: Human-readable primary label for an object.
    comments:
    - Generic reusable naming slot for schema-wide use.
    from_schema: https://w3id.org/reactome-ontology
    rank: 1000
    slot_uri: rdfs:label
    alias: name
    owner: sequence_entity
    domain_of:
    - named_entity
    range: string
  description:
    name: description
    description: Free-text textual description of an object.
    comments:
    - Can hold editorial notes, plain-language explanations, or short summaries.
    from_schema: https://w3id.org/reactome-ontology
    rank: 1000
    slot_uri: dcterms:description
    alias: description
    owner: sequence_entity
    domain_of:
    - named_entity
    range: string
    multivalued: false
class_uri: reactome:SequenceEntity