Class: Protocol (XYZProtocol)

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: dldemoed:XYZProtocol

erDiagram
Annotation {
    string annotation_value  
}
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  
}
Identifier {
    uriorcurie creator  
    string notation  
    NodeUriOrCurie schema_type  
}
Property {
    uriorcurie pid  
    uriorcurieList broad_mappings  
    uriorcurieList close_mappings  
    string description  
    uriorcurieList exact_mappings  
    uriorcurieList narrow_mappings  
    uriorcurieList related_mappings  
    NodeUriOrCurie schema_type  
}
Statement {

}
Thing {
    uriorcurie pid  
    uriorcurieList broad_mappings  
    uriorcurieList close_mappings  
    string description  
    uriorcurieList exact_mappings  
    uriorcurieList narrow_mappings  
    uriorcurieList related_mappings  
    NodeUriOrCurie schema_type  
}
XYZProtocol {
    string name  
    string short_name  
    string display_label  
    string display_note  
    stringList editorial_note  
    uriorcurie pid  
    uriorcurieList broad_mappings  
    uriorcurieList close_mappings  
    string description  
    uriorcurieList exact_mappings  
    uriorcurieList narrow_mappings  
    uriorcurieList related_mappings  
    NodeUriOrCurie schema_type  
}

Annotation ||--|o Thing : "annotation_tag"
AttributeSpecification ||--|| Property : "predicate"
AttributeSpecification ||--}o Annotation : "annotations"
AttributeSpecification ||--}o AttributeSpecification : "attributes"
AttributeSpecification ||--}o Statement : "characterized_by"
Property ||--}o Annotation : "annotations"
Property ||--}o AttributeSpecification : "attributes"
Property ||--}o Statement : "characterized_by"
Property ||--}o Thing : "relations"
Statement ||--|| Property : "predicate"
Statement ||--|| Thing : "object"
Thing ||--}o Annotation : "annotations"
Thing ||--}o AttributeSpecification : "attributes"
Thing ||--}o Statement : "characterized_by"
Thing ||--}o Thing : "relations"
XYZProtocol ||--}o Annotation : "annotations"
XYZProtocol ||--}o AttributeSpecification : "attributes"
XYZProtocol ||--}o Identifier : "identifiers"
XYZProtocol ||--}o Statement : "characterized_by"
XYZProtocol ||--}o Thing : "relations"

Inheritance

Thing [ ThingMixin]
- FlatThing
  - XYZProtocol

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
display_label	0..1 recommended String	Label that can be shown when the metadata record is displayed as an item	FlatThing
display_note	0..1 String	Note that can be shown when the record is displayed as an item	FlatThing
editorial_note	* String	A comment about a metadata record either providing additional information for...	FlatThing
identifiers	* Identifier	An unambiguous reference to the subject within a given context	FlatThing
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
XYZStudy	implements	range	XYZProtocol
XYZStudyActivity	implements	range	XYZProtocol

Identifier and Mapping Information

Schema Source

from schema: https://concepts.datalad.org/s/demo-empirical-data

Mappings

Mapping Type	Mapped Value
self	dldemoed:XYZProtocol
native	dldemoed:XYZProtocol
exact	obo:OBI_0000272

Examples

Example: XYZProtocol-1

description: 'At the time of capture, each adult penguin was quickly blood sampled
  (~1 ml) from the brachial vein using a sterile 3 ml syringe and heparinized infusion
  needle.

  Collected blood was stored in 1.5 ml micro-centrifuge tubes that were kept cool.

  In the field, a small amount of whole blood was smeared on clean filter paper stored
  in a 1.5 ml micro-centrifuge tube for molecular sexing.'
pid: https://example.org/ns/demo/penguins/prot/penguin_blood_sample_collection
display_label: Penguin blood sample collection
name: Penguin blood sample collection

LinkML Source

Direct

name: XYZProtocol
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.
title: Protocol
from_schema: https://concepts.datalad.org/s/demo-empirical-data
exact_mappings:
- obo:OBI_0000272
is_a: FlatThing
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

Induced

name: XYZProtocol
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.
title: Protocol
from_schema: https://concepts.datalad.org/s/demo-empirical-data
exact_mappings:
- obo:OBI_0000272
is_a: FlatThing
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.datalad.org/s/demo-empirical-data
    rank: 1000
    alias: name
    owner: XYZProtocol
    domain_of:
    - XYZOrganization
    - XYZDataset
    - XYZDistribution
    - XYZDimension
    - XYZFactor
    - XYZFileFormat
    - XYZInstrument
    - XYZProtocol
    - XYZStudy
    - XYZSubject
    - XYZSubjectType
    - XYZUnit
    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.datalad.org/s/demo-empirical-data
    rank: 1000
    alias: short_name
    owner: XYZProtocol
    domain_of:
    - XYZOrganization
    - XYZDataset
    - XYZDimension
    - XYZFactor
    - XYZFileFormat
    - XYZInstrument
    - XYZProtocol
    - XYZStudy
    - XYZUnit
    range: string
  display_label:
    name: display_label
    annotations:
      sh:order:
        tag: sh:order
        value: 4
    description: Label that can be shown when the metadata record is displayed as
      an item.
    title: Record display label
    from_schema: https://concepts.datalad.org/s/demo-empirical-data
    rank: 1000
    slot_uri: skos:prefLabel
    alias: display_label
    owner: XYZProtocol
    domain_of:
    - FlatThing
    range: string
    recommended: true
  display_note:
    name: display_note
    annotations:
      dash:singleLine:
        tag: dash:singleLine
        value: false
    description: Note that can be shown when the record is displayed as an item. This
      is typically longer than a label.
    title: Record display note
    from_schema: https://concepts.datalad.org/s/demo-empirical-data
    rank: 1000
    slot_uri: skos:note
    alias: display_note
    owner: XYZProtocol
    domain_of:
    - FlatThing
    range: string
  editorial_note:
    name: editorial_note
    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: Editorial note
    from_schema: https://concepts.datalad.org/s/demo-empirical-data
    rank: 1000
    slot_uri: skos:editorialNote
    alias: editorial_note
    owner: XYZProtocol
    domain_of:
    - FlatThing
    range: string
    multivalued: true
  identifiers:
    name: identifiers
    description: An unambiguous reference to the subject within a given context.
    from_schema: https://concepts.datalad.org/s/demo-empirical-data
    exact_mappings:
    - dcterms:identifier
    - schema:identifier
    - ADMS:identifier
    rank: 1000
    slot_uri: dlidentifiers:identifier
    alias: identifiers
    owner: XYZProtocol
    domain_of:
    - FlatThing
    range: Identifier
    multivalued: true
    inlined: true
    inlined_as_list: true
  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.datalad.org/s/demo-empirical-data
    exact_mappings:
    - dcterms:identifier
    - schema:identifier
    - ADMS:identifier
    rank: 1000
    slot_uri: dlthings:pid
    identifier: true
    alias: pid
    owner: XYZProtocol
    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.datalad.org/s/demo-empirical-data
    exact_mappings:
    - dcat:relation
    - dcterms:relation
    rank: 1000
    domain: Thing
    slot_uri: dlthings:relation
    alias: relations
    owner: XYZProtocol
    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.datalad.org/s/demo-empirical-data
    exact_mappings:
    - obo:NCIT_C44272
    rank: 1000
    slot_uri: dlthings:annotations
    alias: annotations
    owner: XYZProtocol
    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.datalad.org/s/demo-empirical-data
    rank: 1000
    is_a: mappings
    slot_uri: skos:broadMatch
    alias: broad_mappings
    owner: XYZProtocol
    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.datalad.org/s/demo-empirical-data
    rank: 1000
    is_a: mappings
    slot_uri: skos:closeMatch
    alias: close_mappings
    owner: XYZProtocol
    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.datalad.org/s/demo-empirical-data
    exact_mappings:
    - dcterms:description
    - rdfs:comment
    broad_mappings:
    - obo:IAO_0000300
    rank: 1000
    slot_uri: dlthings:description
    alias: description
    owner: XYZProtocol
    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.datalad.org/s/demo-empirical-data
    rank: 1000
    is_a: mappings
    slot_uri: skos:exactMatch
    alias: exact_mappings
    owner: XYZProtocol
    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.datalad.org/s/demo-empirical-data
    exact_mappings:
    - sio:SIO_000008
    rank: 1000
    slot_uri: dlthings:attributes
    alias: attributes
    owner: XYZProtocol
    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.datalad.org/s/demo-empirical-data
    exact_mappings:
    - obo:RO_0000053
    rank: 1000
    slot_uri: dlthings:characterized_by
    alias: characterized_by
    owner: XYZProtocol
    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.datalad.org/s/demo-empirical-data
    rank: 1000
    is_a: mappings
    slot_uri: skos:narrowMatch
    alias: narrow_mappings
    owner: XYZProtocol
    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.datalad.org/s/demo-empirical-data
    rank: 1000
    is_a: mappings
    slot_uri: skos:relatedMatch
    alias: related_mappings
    owner: XYZProtocol
    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.datalad.org/s/demo-empirical-data
    exact_mappings:
    - dcterms:type
    rank: 1000
    slot_uri: rdf:type
    designates_type: true
    alias: schema_type
    owner: XYZProtocol
    domain_of:
    - ThingMixin
    - Identifier
    range: NodeUriOrCurie