Class: Entity

An object retrieved by BERtron from a BER data API.

__

classDiagram class Entity click Entity href "../Entity" Entity : alt_ids Entity : alt_names Entity --> "*" Name : alt_names click Name href "../Name" Entity : ber_data_source Entity --> "1" BERSourceType : ber_data_source click BERSourceType href "../BERSourceType" Entity : coordinates Entity --> "1" Coordinates : coordinates click Coordinates href "../Coordinates" Entity : description Entity : entity_type Entity --> "1..*" EntityType : entity_type click EntityType href "../EntityType" Entity : id Entity : name Entity : part_of_collection Entity --> "*" DataCollection : part_of_collection click DataCollection href "../DataCollection" Entity : uri

Slots

Name	Cardinality and Range	Description	Inheritance
ber_data_source	1 BERSourceType	The BER member from whence the entity originated.	direct
coordinates	1 Coordinates	The geographic coordinates associated with an entity. For entities with a bounding box, the centroid is used as the geographic reference.	direct
entity_type	1..* EntityType	What kind of entity is this -- e.g. sequence data; a soil core; a well; field site; sample; etc.	direct
description	0..1 String	Textual description of the entity.	direct
id	0..1 String	The unique ID used for the entity within the BER resource. It may not necessarily be resolvable outside the resource.	direct
name	0..1 String	Human-readable string representing an entity.	direct
alt_ids	* Uriorcurie	Fully-qualified URI or CURIE used as an identifier for an entity.	direct
alt_names	* Name	Textual identifiers for an entity.	direct
part_of_collection	* DataCollection	Administrative collection (e.g. project, campaign, whatever) that the entity was generated as part of. May also be called a project.	direct
uri	1 Uriorcurie	Permanent resolvable URI for the entity at the data source.	direct

Identifier and Mapping Information

Schema Source

from schema: https://w3id.org/ber-data/bertron-schema

Mappings

Mapping Type	Mapped Value
self	schema:Thing
native	bertron:Entity

LinkML Source

Direct

name: Entity
description: 'An object retrieved by BERtron from a BER data API.

  '
from_schema: https://w3id.org/ber-data/bertron-schema
attributes:
  ber_data_source:
    name: ber_data_source
    description: The BER member from whence the entity originated.
    from_schema: https://w3id.org/ber-data/bertron-schema
    rank: 1000
    domain_of:
    - Entity
    range: BERSourceType
    required: true
  coordinates:
    name: coordinates
    description: The geographic coordinates associated with an entity. For entities
      with a bounding box, the centroid is used as the geographic reference.
    from_schema: https://w3id.org/ber-data/bertron-schema
    rank: 1000
    domain_of:
    - Entity
    range: Coordinates
    required: true
  entity_type:
    name: entity_type
    description: What kind of entity is this -- e.g. sequence data; a soil core; a
      well; field site; sample; etc.
    from_schema: https://w3id.org/ber-data/bertron-schema
    rank: 1000
    domain_of:
    - Entity
    range: EntityType
    required: true
    multivalued: true
  description:
    name: description
    description: Textual description of the entity.
    examples:
    - value: River water sample taken by AquaTROLL 9000.
    - value: Genome sequence of P. aeruginosa strain IDDQD
    from_schema: https://w3id.org/ber-data/bertron-schema
    rank: 1000
    slot_uri: schema:description
    domain_of:
    - Entity
    - DataCollection
    required: false
  id:
    name: id
    description: The unique ID used for the entity within the BER resource. It may
      not necessarily be resolvable outside the resource.
    comments:
    - If the data source does not use CURIEs, we cannot guarantee that IDs will be
      unique between all the BER sources.
    from_schema: https://w3id.org/ber-data/bertron-schema
    aliases:
    - BER data source internal identifier
    - CURIE
    rank: 1000
    slot_uri: schema:identifier
    domain_of:
    - Entity
    - DataCollection
    range: string
  name:
    name: name
    description: Human-readable string representing an entity.
    examples:
    - value: Pseudomonas aeruginosa strain IDDQD
    - value: Soil core FW-106
    from_schema: https://w3id.org/ber-data/bertron-schema
    rank: 1000
    slot_uri: schema:name
    domain_of:
    - Entity
    - Name
    multivalued: false
  alt_ids:
    name: alt_ids
    description: Fully-qualified URI or CURIE used as an identifier for an entity.
    comments:
    - The entity `id` should not appear in this list.
    examples:
    - value: NCBItaxon:172684329
    - value: ISGN:1986497
    from_schema: https://w3id.org/ber-data/bertron-schema
    aliases:
    - CURIEs
    - database cross-references
    - dbxrefs
    - IDs
    - alternative identifiers
    - alternative IDs
    - alternative PIDs
    - PIDs
    rank: 1000
    domain_of:
    - Entity
    - DataCollection
    range: uriorcurie
    multivalued: true
  alt_names:
    name: alt_names
    description: Textual identifiers for an entity.
    comments:
    - The entity `name` should not appear in this list.
    from_schema: https://w3id.org/ber-data/bertron-schema
    aliases:
    - alternative names
    - synonyms
    rank: 1000
    domain_of:
    - Entity
    range: Name
    multivalued: true
  part_of_collection:
    name: part_of_collection
    description: Administrative collection (e.g. project, campaign, whatever) that
      the entity was generated as part of. May also be called a project.
    from_schema: https://w3id.org/ber-data/bertron-schema
    rank: 1000
    domain_of:
    - Entity
    range: DataCollection
    required: false
    multivalued: true
  uri:
    name: uri
    description: Permanent resolvable URI for the entity at the data source.
    from_schema: https://w3id.org/ber-data/bertron-schema
    aliases:
    - url
    rank: 1000
    domain_of:
    - Entity
    range: uriorcurie
    required: true
class_uri: schema:Thing

Induced

name: Entity
description: 'An object retrieved by BERtron from a BER data API.

  '
from_schema: https://w3id.org/ber-data/bertron-schema
attributes:
  ber_data_source:
    name: ber_data_source
    description: The BER member from whence the entity originated.
    from_schema: https://w3id.org/ber-data/bertron-schema
    rank: 1000
    alias: ber_data_source
    owner: Entity
    domain_of:
    - Entity
    range: BERSourceType
    required: true
  coordinates:
    name: coordinates
    description: The geographic coordinates associated with an entity. For entities
      with a bounding box, the centroid is used as the geographic reference.
    from_schema: https://w3id.org/ber-data/bertron-schema
    rank: 1000
    alias: coordinates
    owner: Entity
    domain_of:
    - Entity
    range: Coordinates
    required: true
  entity_type:
    name: entity_type
    description: What kind of entity is this -- e.g. sequence data; a soil core; a
      well; field site; sample; etc.
    from_schema: https://w3id.org/ber-data/bertron-schema
    rank: 1000
    alias: entity_type
    owner: Entity
    domain_of:
    - Entity
    range: EntityType
    required: true
    multivalued: true
  description:
    name: description
    description: Textual description of the entity.
    examples:
    - value: River water sample taken by AquaTROLL 9000.
    - value: Genome sequence of P. aeruginosa strain IDDQD
    from_schema: https://w3id.org/ber-data/bertron-schema
    rank: 1000
    slot_uri: schema:description
    alias: description
    owner: Entity
    domain_of:
    - Entity
    - DataCollection
    range: string
    required: false
  id:
    name: id
    description: The unique ID used for the entity within the BER resource. It may
      not necessarily be resolvable outside the resource.
    comments:
    - If the data source does not use CURIEs, we cannot guarantee that IDs will be
      unique between all the BER sources.
    from_schema: https://w3id.org/ber-data/bertron-schema
    aliases:
    - BER data source internal identifier
    - CURIE
    rank: 1000
    slot_uri: schema:identifier
    alias: id
    owner: Entity
    domain_of:
    - Entity
    - DataCollection
    range: string
  name:
    name: name
    description: Human-readable string representing an entity.
    examples:
    - value: Pseudomonas aeruginosa strain IDDQD
    - value: Soil core FW-106
    from_schema: https://w3id.org/ber-data/bertron-schema
    rank: 1000
    slot_uri: schema:name
    alias: name
    owner: Entity
    domain_of:
    - Entity
    - Name
    range: string
    multivalued: false
  alt_ids:
    name: alt_ids
    description: Fully-qualified URI or CURIE used as an identifier for an entity.
    comments:
    - The entity `id` should not appear in this list.
    examples:
    - value: NCBItaxon:172684329
    - value: ISGN:1986497
    from_schema: https://w3id.org/ber-data/bertron-schema
    aliases:
    - CURIEs
    - database cross-references
    - dbxrefs
    - IDs
    - alternative identifiers
    - alternative IDs
    - alternative PIDs
    - PIDs
    rank: 1000
    alias: alt_ids
    owner: Entity
    domain_of:
    - Entity
    - DataCollection
    range: uriorcurie
    multivalued: true
  alt_names:
    name: alt_names
    description: Textual identifiers for an entity.
    comments:
    - The entity `name` should not appear in this list.
    from_schema: https://w3id.org/ber-data/bertron-schema
    aliases:
    - alternative names
    - synonyms
    rank: 1000
    alias: alt_names
    owner: Entity
    domain_of:
    - Entity
    range: Name
    multivalued: true
  part_of_collection:
    name: part_of_collection
    description: Administrative collection (e.g. project, campaign, whatever) that
      the entity was generated as part of. May also be called a project.
    from_schema: https://w3id.org/ber-data/bertron-schema
    rank: 1000
    alias: part_of_collection
    owner: Entity
    domain_of:
    - Entity
    range: DataCollection
    required: false
    multivalued: true
  uri:
    name: uri
    description: Permanent resolvable URI for the entity at the data source.
    from_schema: https://w3id.org/ber-data/bertron-schema
    aliases:
    - url
    rank: 1000
    alias: uri
    owner: Entity
    domain_of:
    - Entity
    range: uriorcurie
    required: true
class_uri: schema:Thing