Class: Data Item (DataItem)

name: DataItem
description: An Information Entity representing an individual piece of data, generated
  or acquired through methods which reliably produce truthful information about something.
title: Data Item
comments:
- Examples include raw observations or measurements such as an allele count, or patient's
  weight, derived calculations such as frequency or mean, and computed statistical
  scores/metrics such as p-values and z-scores.
from_schema: https://w3id.org/sepio-framework/sepio-linkml
status: Informative
is_a: InformationEntity
attributes:
  subtype:
    name: subtype
    description: A specific type of data the DataItem instance represents (e.g. a
      'specimen count', a 'patient weight', an 'allele frequency', a 'p-value')
    comments:
    - This attribute can be used to report a specific type for the DataItem, in cases
      where a model does not define DataItem subclasses for this purpose.  Implementers
      can define their own set of data item type codes/terms, to match the needs of
      the domain or application.
    from_schema: https://w3id.org/sepio-model
    status: Informative
    domain_of:
    - Method
    - Document
    - DataItem
    - DataSet
    - Activity
    - Agent
    - EvidenceLine
    range: Coding
    required: false
    multivalued: false
  value:
    name: value
    description: The value of the data item (could be quantitative or qualitative
      depending on the type of data item).
    from_schema: https://w3id.org/sepio-model
    status: Informative
    rank: 1000
    domain_of:
    - DataItem
    - Qualifier
    - Expression
    - Extension
    range: string
    required: true
    multivalued: false
  unit:
    name: unit
    description: A unit of measure for the value (e.g. meters, grams, fluorescent
      units, seconds, mg/ml, etc.)
    comments:
    - Implementers should define a relevant source or specific set of unit terms/codes
      to use here based on the needs of the domain or application.
    from_schema: https://w3id.org/sepio-model
    status: Informative
    rank: 1000
    domain_of:
    - DataItem
    range: Coding
    required: false
    multivalued: false
  variabilityMeasures:
    name: variabilityMeasures
    description: A statistical score describing the variability inherent in a data
      item representing a statistical summary of a set of observations/measurements
      (e.g. the standard deviation associated with a statistical mean calculated across
      several experimental replicates).
    comments:
    - Examples of statistical measures of variability include an Interquartile Range,
      Variance, Standard Deviation, Standard Error. The type of variability measure
      used here represents should be reported in the DataItem instance created to
      represent it.
    from_schema: https://w3id.org/sepio-model
    status: Informative
    rank: 1000
    domain_of:
    - DataItem
    range: DataItem
    required: false
    multivalued: true
  confidenceInterval:
    name: confidenceInterval
    description: A measure of the probability that a parameter of interest will fall
      within a defined range of values around a mean or other statistical calculation.
    comments:
    - Confidence intervals reflect the degree of uncertainty in a sampling method.
      They may be bounded on one or both sides, and are  computed for a designated
      confidence level (most often 95% or 99%.. For example, a Hazard Ratio of 0.47
      might have a 95% confidence interval between 0.42 and 0.55, with a p-value of
      = 0.001.
    - The DataItem used to represent a confidence interval will indicate what type
      of interval is reported (e.g. ''95% CI''), and will contain separate componentDataItems
      representing the upper and lower bounds of the interval (e.g. ''0.42'' and ''0.55'').'
    from_schema: https://w3id.org/sepio-model
    status: Informative
    rank: 1000
    domain_of:
    - DataItem
    range: DataItem
    required: false
    multivalued: false
  componentDataItem:
    name: componentDataItem
    description: A more foundational data item that is a logical component of a compound
      data item.
    comments:
    - Examples of 'compound' data items with component parts include a confidence
      interval, which is comprised of data items representing its lower and upper
      bounds,  or a blood pressure reading, which is comprised of separate systolic
      and diastolic measurements.
    from_schema: https://w3id.org/sepio-model
    status: Informative
    rank: 1000
    domain_of:
    - DataItem
    range: DataItem
    required: false
    multivalued: true

name: DataItem
description: An Information Entity representing an individual piece of data, generated
  or acquired through methods which reliably produce truthful information about something.
title: Data Item
comments:
- Examples include raw observations or measurements such as an allele count, or patient's
  weight, derived calculations such as frequency or mean, and computed statistical
  scores/metrics such as p-values and z-scores.
from_schema: https://w3id.org/sepio-framework/sepio-linkml
status: Informative
is_a: InformationEntity
attributes:
  subtype:
    name: subtype
    description: A specific type of data the DataItem instance represents (e.g. a
      'specimen count', a 'patient weight', an 'allele frequency', a 'p-value')
    comments:
    - This attribute can be used to report a specific type for the DataItem, in cases
      where a model does not define DataItem subclasses for this purpose.  Implementers
      can define their own set of data item type codes/terms, to match the needs of
      the domain or application.
    from_schema: https://w3id.org/sepio-model
    status: Informative
    alias: subtype
    owner: DataItem
    domain_of:
    - Method
    - Document
    - DataItem
    - DataSet
    - Activity
    - Agent
    - EvidenceLine
    range: Coding
    required: false
    multivalued: false
  value:
    name: value
    description: The value of the data item (could be quantitative or qualitative
      depending on the type of data item).
    from_schema: https://w3id.org/sepio-model
    status: Informative
    rank: 1000
    alias: value
    owner: DataItem
    domain_of:
    - DataItem
    - Qualifier
    - Expression
    - Extension
    range: string
    required: true
    multivalued: false
  unit:
    name: unit
    description: A unit of measure for the value (e.g. meters, grams, fluorescent
      units, seconds, mg/ml, etc.)
    comments:
    - Implementers should define a relevant source or specific set of unit terms/codes
      to use here based on the needs of the domain or application.
    from_schema: https://w3id.org/sepio-model
    status: Informative
    rank: 1000
    alias: unit
    owner: DataItem
    domain_of:
    - DataItem
    range: Coding
    required: false
    multivalued: false
  variabilityMeasures:
    name: variabilityMeasures
    description: A statistical score describing the variability inherent in a data
      item representing a statistical summary of a set of observations/measurements
      (e.g. the standard deviation associated with a statistical mean calculated across
      several experimental replicates).
    comments:
    - Examples of statistical measures of variability include an Interquartile Range,
      Variance, Standard Deviation, Standard Error. The type of variability measure
      used here represents should be reported in the DataItem instance created to
      represent it.
    from_schema: https://w3id.org/sepio-model
    status: Informative
    rank: 1000
    alias: variabilityMeasures
    owner: DataItem
    domain_of:
    - DataItem
    range: DataItem
    required: false
    multivalued: true
  confidenceInterval:
    name: confidenceInterval
    description: A measure of the probability that a parameter of interest will fall
      within a defined range of values around a mean or other statistical calculation.
    comments:
    - Confidence intervals reflect the degree of uncertainty in a sampling method.
      They may be bounded on one or both sides, and are  computed for a designated
      confidence level (most often 95% or 99%.. For example, a Hazard Ratio of 0.47
      might have a 95% confidence interval between 0.42 and 0.55, with a p-value of
      = 0.001.
    - The DataItem used to represent a confidence interval will indicate what type
      of interval is reported (e.g. ''95% CI''), and will contain separate componentDataItems
      representing the upper and lower bounds of the interval (e.g. ''0.42'' and ''0.55'').'
    from_schema: https://w3id.org/sepio-model
    status: Informative
    rank: 1000
    alias: confidenceInterval
    owner: DataItem
    domain_of:
    - DataItem
    range: DataItem
    required: false
    multivalued: false
  componentDataItem:
    name: componentDataItem
    description: A more foundational data item that is a logical component of a compound
      data item.
    comments:
    - Examples of 'compound' data items with component parts include a confidence
      interval, which is comprised of data items representing its lower and upper
      bounds,  or a blood pressure reading, which is comprised of separate systolic
      and diastolic measurements.
    from_schema: https://w3id.org/sepio-model
    status: Informative
    rank: 1000
    alias: componentDataItem
    owner: DataItem
    domain_of:
    - DataItem
    range: DataItem
    required: false
    multivalued: true
  isAbout:
    name: isAbout
    description: An entity or concept in the world that the information entity describes/is
      about.
    comments:
    - e.g. In the context of a Statement object, this attribute may be used to indicate
      entities/concepts it is about, in lieu of providing a more precise description
      of what the Statement asserts to be true using subject, predicate, object, and
      qualifier properties. e.g. the Statement that "BRCA2 c.8023A>G is pathogenic
      for Breast Cancer" might be annotated to be about the variant 'BRCA2 c.8023A>G',
      and the disease 'Breast Cancer'.
    from_schema: https://w3id.org/sepio-model
    status: Informative
    rank: 1000
    alias: isAbout
    owner: DataItem
    domain_of:
    - InformationEntity
    range: string
    required: false
    multivalued: true
  contributions:
    name: contributions
    description: Specific actions taken by an Agent toward the creation, modification,
      validation, or deprecation of an Information Entity.
    comments:
    - This attribute holds one or more Contribution objects, which provide structured
      descriptions of a contribution made to the Information Entity by a particular
      agent.
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    alias: contributions
    owner: DataItem
    domain_of:
    - InformationEntity
    - RecordMetadata
    range: Contribution
    required: false
    multivalued: true
  dateAuthored:
    name: dateAuthored
    description: Indicates when the information content expressed in the Information
      Entity was generated.
    comments:
    - The term 'authored' as used in the model refers to the generation of 'information
      content' in the abstract  sense, as opposed to a concrete encoding of this information
      in a specific language or format. e.g. for a Statement, this attribute captures
      when the information content expressed in the Statement was first generated
      by an agent.  Information about when a particular concrete encoding of this
      information was created (e.g. as row in a table, or object in a json document)
      would live in a RecordMetadata object attached to the Information Entity).
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    alias: dateAuthored
    owner: DataItem
    domain_of:
    - InformationEntity
    range: string
    required: false
    multivalued: false
  specifiedBy:
    name: specifiedBy
    description: A specification that describes all or part of the process that led
      to creation of the Information Entity.
    comments:
    - Examples - an experimental protocol or data analysis specification that describe
      how data were generated, or an evidence interpretation guideline that describes
      steps taken to interpret data in making a variant pathogenicity classification.
    - Note that this attribute captures specific *instances* of specifications/methods
      (e.g. the specific electron microscopy method described in https://doi.org/10.1002/
      cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. "Transmission
      Electron Microscopy").
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    alias: specifiedBy
    owner: DataItem
    domain_of:
    - InformationEntity
    - Activity
    range: string
    required: false
    multivalued: true
  supportingMethods:
    name: supportingMethods
    description: Specific methods that were executed to directly or indirectly support
      creation of the Information Entity.
    comments:
    - These may include methods that directly produced the Information Entity, or
      upstream/accessory methods that indirectly support creation of the Information
      Entity - e.g. methods used to produce data that was interpreted as evidence
      to generate a Statement of knowledge.
    - This field captures terms representing specific INSTANCES of methods applied,
      vs the 'supportingMethodTypes' attribute which captures TYPES of methods used.
    from_schema: https://w3id.org/sepio-model
    status: Informative
    rank: 1000
    alias: supportingMethods
    owner: DataItem
    domain_of:
    - InformationEntity
    range: string
    required: false
    multivalued: true
  supportingMethodTypes:
    name: supportingMethodTypes
    description: Types of methodological approaches that were executed to directly
      or indirectly support creation of the Information Entity.
    comments:
    - This field captures terms representing TYPES of methods applied, vs the 'specifiedBy'
      or'supportingMethods' attributes which capture specific INSTANCES of methods
      used. These may include types of methods that directly produced the Information
      Entity, or upstream/accessory methods that indirectly support creation of the
      Information Entity
    - Implementers should define a relevant source or set of method type codes/terms
      to use here, based on the needs of the domain or application.'
    from_schema: https://w3id.org/sepio-model
    status: Informative
    rank: 1000
    alias: supportingMethodTypes
    owner: DataItem
    domain_of:
    - InformationEntity
    range: Coding
    required: false
    multivalued: true
  derivedFrom:
    name: derivedFrom
    description: Another Information Entity from which this Information Entity is
      derived, in whole or in part.
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    alias: derivedFrom
    owner: DataItem
    domain_of:
    - InformationEntity
    range: InformationEntity
    required: false
    multivalued: true
  reportedIn:
    name: reportedIn
    description: A document in which the Information Entity is reported.
    comments:
    - This attribute is used specifically to reference documents/publications where
      the Information Entity is expressed or reported.  For a Statement, this might
      be a publication where the authors express the statement in text. For a Data
      Item, this might be a publication with a table or figure that reports the value
      of the  data.
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    alias: reportedIn
    owner: DataItem
    domain_of:
    - InformationEntity
    range: string
    required: false
    multivalued: true
  sources:
    name: sources
    description: A document or other informtion resource in which the information
      entity, or evidence supporting it, is reported.
    comments:
    - This attribute is more general than InformationEntity.reportedIn (which is used
      to references a Docuement that directly reports the infrormation), and Statement.hasEvidenceFromSources
      (which is used to reference resources that provided evidence used to generate
      the knowledge expressed in a Statement). It can be used to cover both cases,
      in situations where a data provider does not know which is the case, or does
      not wish to make the distinction.
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    alias: sources
    owner: DataItem
    domain_of:
    - InformationEntity
    range: string
    required: false
    multivalued: true
  informationQuality:
    name: informationQuality
    description: A qualitative term indicating the scientific rigor or reliability
      with which the information was generated/collected.
    comments:
    - This is typically based on the quality of design and execution of the study
      or curation activity that generated it (e.g. were relevant controls assessed
      to show instruments were working, were all samples taken care of and handled
      identically, are methods sound and well documented, etc.).
    - The quality of information is intrinsic to the information itself, and not to
      a particular application of the information (e.g. as evidence for making an
      Assertion)
    - The quality of information is one factor that goes into the confidence we have
      in the information''s veracity (i.e. that it is an accurate reflection of reality
      it intends to measure or describe). Other factors informing confidence may include
      who did it (we may just not trust some Agents), when (if data created 500 years
      ago, we may have less confidence in it), and for Assertions, the relevance and
      abundance of supporting evidence.
    - Implementers should define a relevant source of codes or terms to use here,
      based on the needs of the domain or application.'
    from_schema: https://w3id.org/sepio-model
    status: Informative
    rank: 1000
    alias: informationQuality
    owner: DataItem
    domain_of:
    - InformationEntity
    range: Coding
    required: false
    multivalued: false
  recordMetadata:
    name: recordMetadata
    description: Provenance metadata about a specific concrete record of information
      as encoded/serialized in a particular data set or object (as opposed to provenance
      about the abstract information content the encoding carries).
    comments:
    - This attribute holds a structured RecordMetadata objects, which can be used
      to capture when, how, and by whom a record serialization was generated or modified;
      what upstream resources it was derived or retrieved from; and record-level administrative
      information such as versioning and lifecycle status.
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    alias: recordMetadata
    owner: DataItem
    domain_of:
    - InformationEntity
    range: RecordMetadata
    required: false
    multivalued: false
  id:
    name: id
    description: The 'logical' identifier of the entity in the system of record, e.g.
      a UUID.  This 'id' is unique within a given system, but may or may not be globally
      unique outside the system. It is used within a system to reference one object
      from another.
    comments:
    - Note that it is common for implementers to create their own internal logical
      ids - typically a serially or randomly generated value like a UUID that is assigned
      to the data object as it is created in a system. But an implementer may choose
      to reuse an existing, globally unique id from an external system or authority
      for this purpose (e.g. an HGNC id for a Gene object) - as long as it is unique
      within the implementing system, and can be used to reference the identified
      object in this context.
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    alias: id
    owner: DataItem
    domain_of:
    - Entity
    range: string
    required: true
    multivalued: false
  identifiers:
    name: identifiers
    description: A globally-unique 'business' identifier or accession number for the
      real-world entity represented by a data object. These are typically assigned
      by an external system or authority, and used to connect entities and share content
      across different systems.
    comments:
    - Preferred values for this attribute are CURIEs or URIs - so the system that
      provisioned the identifier is clear.
    - A given real world entity - e.g. a genetic variant - may have many business
      identifiers defined by different systems, which can be captured in the "identifiers"
      property to indicate that they represent the same thing.
    from_schema: https://w3id.org/sepio-model
    status: Informative
    rank: 1000
    alias: identifiers
    owner: DataItem
    domain_of:
    - Entity
    range: string
    required: false
    multivalued: true
  type:
    name: type
    description: The name of the class that is instantiated by a data object representing
      the Entity.
    comments:
    - MUST be the label of a concrete class from the data model.
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    alias: type
    owner: DataItem
    domain_of:
    - Entity
    range: string
    required: true
    multivalued: false
  label:
    name: label
    description: A primary name for the Entity.
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    alias: label
    owner: DataItem
    domain_of:
    - Entity
    - Coding
    range: string
    required: false
    multivalued: false
  alternativeLabels:
    name: alternativeLabels
    description: Alternative name(s) for the Entity.
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    alias: alternativeLabels
    owner: DataItem
    domain_of:
    - Entity
    range: string
    required: false
    multivalued: true
  description:
    name: description
    description: A free text description of the Entity.
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    alias: description
    owner: DataItem
    domain_of:
    - Entity
    range: string
    required: false
    multivalued: false
  extensions:
    name: extensions
    description: A list of extensions to the Entity, that allow for capture of information
      not directly supported by elements defined in the model.
    comments:
    - Extension objects have a key-value data structure that allows definition of
      custom fields in the data itself. Extensions are not expected to be natively
      understood, but may be used for pre-negotiated exchange of message attributes
      between systems.
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    alias: extensions
    owner: DataItem
    domain_of:
    - Entity
    range: Extension
    required: false
    multivalued: true