Class: Protocol

A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process.

URI: inm7fd:Protocol

erDiagram Protocol { string name string short_name stringList curation_comments string display_label uriorcurie pid uriorcurieList broad_mappings uriorcurieList close_mappings string description uriorcurieList exact_mappings uriorcurieList narrow_mappings uriorcurieList related_mappings NodeUriOrCurie schema_type } Statement { } Property { uriorcurie pid uriorcurieList broad_mappings uriorcurieList close_mappings string description uriorcurieList exact_mappings uriorcurieList narrow_mappings uriorcurieList related_mappings NodeUriOrCurie schema_type } Thing { uriorcurie pid uriorcurieList broad_mappings uriorcurieList close_mappings string description uriorcurieList exact_mappings uriorcurieList narrow_mappings uriorcurieList related_mappings NodeUriOrCurie schema_type } AttributeSpecification { uriorcurieList broad_mappings uriorcurieList close_mappings string description uriorcurieList exact_mappings uriorcurieList narrow_mappings uriorcurieList related_mappings NodeUriOrCurie schema_type uriorcurie range string value } Annotation { string annotation_value } Person { stringList additional_names string family_name string given_name string honorific_name_prefix string honorific_name_suffix EmailAddressList emails string orcid stringList curation_comments string display_label uriorcurie pid uriorcurieList broad_mappings uriorcurieList close_mappings string description uriorcurieList exact_mappings uriorcurieList narrow_mappings uriorcurieList related_mappings NodeUriOrCurie schema_type } Identifier { uriorcurie creator string notation NodeUriOrCurie schema_type } Organization { string name string short_name OrganizationType organization_type stringList curation_comments string display_label uriorcurie pid uriorcurieList broad_mappings uriorcurieList close_mappings string description uriorcurieList exact_mappings uriorcurieList narrow_mappings uriorcurieList related_mappings NodeUriOrCurie schema_type } Protocol ||--}o Identifier : "identifiers" Protocol ||--|o Person : "record_contact" Protocol ||--}o Thing : "relations" Protocol ||--}o Annotation : "annotations" Protocol ||--}o AttributeSpecification : "attributes" Protocol ||--}o Statement : "characterized_by" Statement ||--|| Thing : "object" Statement ||--|| Property : "predicate" Property ||--}o Thing : "relations" Property ||--}o Annotation : "annotations" Property ||--}o AttributeSpecification : "attributes" Property ||--}o Statement : "characterized_by" Thing ||--}o Thing : "relations" Thing ||--}o Annotation : "annotations" Thing ||--}o AttributeSpecification : "attributes" Thing ||--}o Statement : "characterized_by" AttributeSpecification ||--|| Property : "predicate" AttributeSpecification ||--}o Annotation : "annotations" AttributeSpecification ||--}o AttributeSpecification : "attributes" AttributeSpecification ||--}o Statement : "characterized_by" Annotation ||--|o Thing : "annotation_tag" Person ||--}o Organization : "member_of" Person ||--}o Identifier : "identifiers" Person ||--|o Person : "record_contact" Person ||--}o Thing : "relations" Person ||--}o Annotation : "annotations" Person ||--}o AttributeSpecification : "attributes" Person ||--}o Statement : "characterized_by" Organization ||--|o Organization : "parent_organization" Organization ||--}o Person : "leaders" Organization ||--}o Identifier : "identifiers" Organization ||--|o Person : "record_contact" Organization ||--}o Thing : "relations" Organization ||--}o Annotation : "annotations" Organization ||--}o AttributeSpecification : "attributes" Organization ||--}o Statement : "characterized_by"

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Inheritance

Thing [ ThingMixin]
- Protocol [ CurationAid]

Slots

Name	Cardinality and Range	Description	Inheritance
name	0..1 recommended String	Name of the subject	direct
short_name	0..1 String	A shortened name for the subject	direct
curation_comments	* String	A comment about a metadata record either providing additional information for...	CurationAid
display_label	0..1 recommended String	Label to shown when the record is displayed as an item	CurationAid
identifiers	* Identifier	An unambiguous reference to the subject within a given context	CurationAid
record_contact	0..1 Person	Person to contact regarding questions about information in this metadata reco...	CurationAid
pid	1 Uriorcurie	Persistent and globally unique identifier of a `Thing`	Thing
relations	* Thing	Declares an unqualified relation of the subject `Thing` to another `Thing`	Thing
annotations	* Annotation	A record of properties of the metadata record on a subject, a collection of t...	ThingMixin
broad_mappings	* Uriorcurie	A list of terms from different schemas or terminology systems that have broad...	ThingMixin
close_mappings	* Uriorcurie	A list of terms from different schemas or terminology systems that have close...	ThingMixin
description	0..1 String	A free-text account of the subject	ThingMixin
exact_mappings	* Uriorcurie	A list of terms from different schemas or terminology systems that have ident...	ThingMixin
attributes	* AttributeSpecification	Declares a relation that associates a `Thing` (or another attribute) with an ...	ThingMixin
characterized_by	* Statement	Qualifies relationships between a subject `Thing` and an object `Thing` with ...	ThingMixin
narrow_mappings	* Uriorcurie	A list of terms from different schemas or terminology systems that have narro...	ThingMixin
related_mappings	* Uriorcurie	A list of terms from different schemas or terminology systems that have relat...	ThingMixin
schema_type	0..1 NodeUriOrCurie	State that the subject is an instance of a particular schema class	ThingMixin

Usages

used by	used in	type	used
Study	implements	range	Protocol
StudyActivity	implements	range	Protocol

Identifier and Mapping Information

Schema Source

from schema: https://concepts.inm7.de/s/flat-data/unreleased

Mappings

Mapping Type	Mapped Value
self	inm7fd:Protocol
native	inm7fd:Protocol
exact	obo:OBI_0000272

LinkML Source

Direct

name: Protocol
description: A plan specification which has sufficient level of detail and quantitative
  information to communicate it between investigation agents, so that different investigation
  agents will reliably be able to independently reproduce the process.
from_schema: https://concepts.inm7.de/s/flat-data/unreleased
exact_mappings:
- obo:OBI_0000272
is_a: Thing
mixins:
- CurationAid
slots:
- name
- short_name
slot_usage:
  name:
    name: name
    annotations:
      sh:order:
        tag: sh:order
        value: 1
    recommended: true
  short_name:
    name: short_name
    annotations:
      sh:order:
        tag: sh:order
        value: 2
  description:
    name: description
    annotations:
      sh:order:
        tag: sh:order
        value: 3
      dash:singleLine:
        tag: dash:singleLine
        value: false
  display_label:
    name: display_label
    annotations:
      sh:order:
        tag: sh:order
        value: 4
    recommended: true
class_uri: inm7fd:Protocol

Induced

name: Protocol
description: A plan specification which has sufficient level of detail and quantitative
  information to communicate it between investigation agents, so that different investigation
  agents will reliably be able to independently reproduce the process.
from_schema: https://concepts.inm7.de/s/flat-data/unreleased
exact_mappings:
- obo:OBI_0000272
is_a: Thing
mixins:
- CurationAid
slot_usage:
  name:
    name: name
    annotations:
      sh:order:
        tag: sh:order
        value: 1
    recommended: true
  short_name:
    name: short_name
    annotations:
      sh:order:
        tag: sh:order
        value: 2
  description:
    name: description
    annotations:
      sh:order:
        tag: sh:order
        value: 3
      dash:singleLine:
        tag: dash:singleLine
        value: false
  display_label:
    name: display_label
    annotations:
      sh:order:
        tag: sh:order
        value: 4
    recommended: true
attributes:
  name:
    name: name
    annotations:
      sh:order:
        tag: sh:order
        value: 1
    description: Name of the subject.
    title: Name
    from_schema: https://concepts.inm7.de/s/flat-data/unreleased
    rank: 1000
    alias: name
    owner: Protocol
    domain_of:
    - Dataset
    - Distribution
    - Dimension
    - Factor
    - FileFormat
    - Instrument
    - Protocol
    - Study
    - Subject
    - SubjectType
    - Unit
    - Site
    - Building
    - BuildingLevel
    - Organization
    - Room
    range: string
    recommended: true
  short_name:
    name: short_name
    annotations:
      sh:order:
        tag: sh:order
        value: 2
    description: A shortened name for the subject. For example, an acronym, initialism,
      nickname, or other abbreviation of the name or title.
    title: Short name
    from_schema: https://concepts.inm7.de/s/flat-data/unreleased
    rank: 1000
    alias: short_name
    owner: Protocol
    domain_of:
    - Dataset
    - Dimension
    - Factor
    - FileFormat
    - Instrument
    - Protocol
    - Study
    - Unit
    - Organization
    range: string
  curation_comments:
    name: curation_comments
    annotations:
      dash:singleLine:
        tag: dash:singleLine
        value: false
    description: A comment about a metadata record either providing additional information
      for a record curation, or leaving a comment after curation occurred. This can
      be used to include information that is deemed relevant, but could not be expressed
      in the provided fields.
    title: Comments
    from_schema: https://concepts.inm7.de/s/flat-data/unreleased
    rank: 1000
    alias: curation_comments
    owner: Protocol
    domain_of:
    - CurationAid
    range: string
    multivalued: true
  display_label:
    name: display_label
    annotations:
      sh:order:
        tag: sh:order
        value: 4
    description: Label to shown when the record is displayed as an item.
    title: Record display label
    from_schema: https://concepts.inm7.de/s/flat-data/unreleased
    rank: 1000
    slot_uri: skos:prefLabel
    alias: display_label
    owner: Protocol
    domain_of:
    - CurationAid
    range: string
    recommended: true
  identifiers:
    name: identifiers
    description: An unambiguous reference to the subject within a given context.
    from_schema: https://concepts.inm7.de/s/flat-data/unreleased
    exact_mappings:
    - dcterms:identifier
    - schema:identifier
    - ADMS:identifier
    rank: 1000
    slot_uri: dlidentifiers:identifier
    alias: identifiers
    owner: Protocol
    domain_of:
    - CurationAid
    range: Identifier
    multivalued: true
    inlined: true
    inlined_as_list: true
  record_contact:
    name: record_contact
    description: Person to contact regarding questions about information in this metadata
      record.
    title: Record contact
    from_schema: https://concepts.inm7.de/s/flat-data/unreleased
    rank: 1000
    alias: record_contact
    owner: Protocol
    domain_of:
    - CurationAid
    range: Person
  pid:
    name: pid
    annotations:
      sh:order:
        tag: sh:order
        value: 1
    description: Persistent and globally unique identifier of a `Thing`.
    title: Persistent identifier
    from_schema: https://concepts.inm7.de/s/flat-data/unreleased
    exact_mappings:
    - dcterms:identifier
    - schema:identifier
    - ADMS:identifier
    rank: 1000
    slot_uri: dlthings:pid
    identifier: true
    alias: pid
    owner: Protocol
    domain_of:
    - Thing
    range: uriorcurie
    required: true
  relations:
    name: relations
    annotations:
      sh:order:
        tag: sh:order
        value: 6
    description: Declares an unqualified relation of the subject `Thing` to another
      `Thing`. This schema slot is used to define related things inline. If such a
      definition is not needed. A qualified relationship can be declared directly
      using the `characterized_by` slot.
    title: Relations
    from_schema: https://concepts.inm7.de/s/flat-data/unreleased
    exact_mappings:
    - dcat:relation
    - dcterms:relation
    rank: 1000
    domain: Thing
    slot_uri: dlthings:relation
    alias: relations
    owner: Protocol
    domain_of:
    - Thing
    symmetric: true
    relational_role: OBJECT
    range: Thing
    multivalued: true
    inlined: true
    inlined_as_list: false
  annotations:
    name: annotations
    annotations:
      sh:order:
        tag: sh:order
        value: 5
    description: A record of properties of the metadata record on a subject, a collection
      of tag/text tuples with the semantics of OWL Annotation.
    title: Annotations
    from_schema: https://concepts.inm7.de/s/flat-data/unreleased
    exact_mappings:
    - obo:NCIT_C44272
    rank: 1000
    slot_uri: dlthings:annotations
    alias: annotations
    owner: Protocol
    domain_of:
    - ThingMixin
    range: Annotation
    multivalued: true
    inlined: true
  broad_mappings:
    name: broad_mappings
    annotations:
      sh:order:
        tag: sh:order
        value: 9
    description: A list of terms from different schemas or terminology systems that
      have broader meaning.
    title: Broad mappings
    from_schema: https://concepts.inm7.de/s/flat-data/unreleased
    rank: 1000
    is_a: mappings
    slot_uri: skos:broadMatch
    alias: broad_mappings
    owner: Protocol
    domain_of:
    - ThingMixin
    range: uriorcurie
    multivalued: true
  close_mappings:
    name: close_mappings
    annotations:
      sh:order:
        tag: sh:order
        value: 8
    description: A list of terms from different schemas or terminology systems that
      have close meaning.
    title: Close mappings
    from_schema: https://concepts.inm7.de/s/flat-data/unreleased
    rank: 1000
    is_a: mappings
    slot_uri: skos:closeMatch
    alias: close_mappings
    owner: Protocol
    domain_of:
    - ThingMixin
    range: uriorcurie
    multivalued: true
  description:
    name: description
    annotations:
      sh:order:
        tag: sh:order
        value: 3
      dash:singleLine:
        tag: dash:singleLine
        value: false
    description: A free-text account of the subject.
    title: Description
    from_schema: https://concepts.inm7.de/s/flat-data/unreleased
    exact_mappings:
    - dcterms:description
    - rdfs:comment
    broad_mappings:
    - obo:IAO_0000300
    rank: 1000
    slot_uri: dlthings:description
    alias: description
    owner: Protocol
    domain_of:
    - ThingMixin
    range: string
  exact_mappings:
    name: exact_mappings
    annotations:
      sh:order:
        tag: sh:order
        value: 7
    description: A list of terms from different schemas or terminology systems that
      have identical meaning.
    title: Exact mappings
    from_schema: https://concepts.inm7.de/s/flat-data/unreleased
    rank: 1000
    is_a: mappings
    slot_uri: skos:exactMatch
    alias: exact_mappings
    owner: Protocol
    domain_of:
    - ThingMixin
    range: uriorcurie
    multivalued: true
  attributes:
    name: attributes
    annotations:
      sh:order:
        tag: sh:order
        value: 3
    description: Declares a relation that associates a `Thing` (or another attribute)
      with an attribute, where an attribute is an intrinsic characteristic, such as
      a quality, capability, disposition, function, or is an externally derived attribute
      determined from some descriptor (e.g. a quantity, position, label/identifier).
      Technically, this declaration is done via an `AttributeSpecification` that combines
      a `predicate` with a value declaration and the attribute-related slots of a
      `Thing`. Importantly, such attributes are declared inline, because they do not
      have a unique identifier. If an identifier is available, a `Thing` declaration
      (see `relation`), and a qualification of that relationship via a `Statement`
      (see `characterized_by`) should be preferred.
    title: Attributes
    from_schema: https://concepts.inm7.de/s/flat-data/unreleased
    exact_mappings:
    - sio:SIO_000008
    rank: 1000
    slot_uri: dlthings:attributes
    alias: attributes
    owner: Protocol
    domain_of:
    - ThingMixin
    range: AttributeSpecification
    multivalued: true
    inlined: true
    inlined_as_list: true
  characterized_by:
    name: characterized_by
    annotations:
      sh:order:
        tag: sh:order
        value: 2
    description: Qualifies relationships between a subject `Thing` and an object `Thing`
      with a `Statement` declaring a `predicate` on the nature of the relationship.
    title: Is characterized by
    from_schema: https://concepts.inm7.de/s/flat-data/unreleased
    exact_mappings:
    - obo:RO_0000053
    rank: 1000
    slot_uri: dlthings:characterized_by
    alias: characterized_by
    owner: Protocol
    domain_of:
    - ThingMixin
    range: Statement
    multivalued: true
    inlined: true
    inlined_as_list: true
  narrow_mappings:
    name: narrow_mappings
    annotations:
      sh:order:
        tag: sh:order
        value: 10
    description: A list of terms from different schemas or terminology systems that
      have narrower meaning.
    title: Narrow mappings
    from_schema: https://concepts.inm7.de/s/flat-data/unreleased
    rank: 1000
    is_a: mappings
    slot_uri: skos:narrowMatch
    alias: narrow_mappings
    owner: Protocol
    domain_of:
    - ThingMixin
    range: uriorcurie
    multivalued: true
  related_mappings:
    name: related_mappings
    annotations:
      sh:order:
        tag: sh:order
        value: 11
    description: A list of terms from different schemas or terminology systems that
      have related meaning.
    title: Related mappings
    from_schema: https://concepts.inm7.de/s/flat-data/unreleased
    rank: 1000
    is_a: mappings
    slot_uri: skos:relatedMatch
    alias: related_mappings
    owner: Protocol
    domain_of:
    - ThingMixin
    range: uriorcurie
    multivalued: true
  schema_type:
    name: schema_type
    description: State that the subject is an instance of a particular schema class.
      Typically, no explicit value needs to be assigned to this slot, because it matches
      the class type of a particular record. However, this slots can be used as a
      type designator of a schema element for validation and schema structure handling
      purposes. This is used to indicate specialized schema classes for properties
      that accept a hierarchy of classes as their range.
    from_schema: https://concepts.inm7.de/s/flat-data/unreleased
    exact_mappings:
    - dcterms:type
    rank: 1000
    slot_uri: rdf:type
    designates_type: true
    alias: schema_type
    owner: Protocol
    domain_of:
    - ThingMixin
    - Identifier
    range: NodeUriOrCurie
class_uri: inm7fd:Protocol