Class: Study

Default Study description

URI: https://github.com/vdjserver/vdjserver-airr-schema/Study

 classDiagram
    class Study
    click Study href "../Study/"
      AIRRStandards <|-- Study
        click AIRRStandards href "../AIRRStandards/"

      Study : adc_publish_date

      Study : adc_update_date

      Study : contributors





        Study --> "*" Contributor : contributors
        click Contributor href "../Contributor/"



      Study : grants

      Study : inclusion_exclusion_criteria

      Study : keywords_study





        Study --> "*" KeywordsStudyEnum : keywords_study
        click KeywordsStudyEnum href "../KeywordsStudyEnum/"



      Study : pub_ids

      Study : study_description

      Study : study_id

      Study : study_title

      Study : study_type





        Study --> "0..1" StudyTypeOntology : study_type
        click StudyTypeOntology href "../StudyTypeOntology/"

Inheritance

AIRRStandards
- Study

Slots

Name	Cardinality and Range	Description	Inheritance
study_id	0..1 String	Unique ID assigned by study registry such as one of the International Nucleot...	direct
study_title	0..1 String	Descriptive study title	direct
study_type	0..1 StudyTypeOntology	Type of study design	direct
study_description	0..1 String	Generic study description	direct
inclusion_exclusion_criteria	0..1 String	List of criteria for inclusion/exclusion for the study	direct
grants	0..1 String	Funding agencies and grant numbers	direct
contributors	* Contributor	List of individuals who contributed to the study	direct
pub_ids	* String		direct
keywords_study	* KeywordsStudyEnum	Keywords describing properties of one or more data sets in a study	direct
adc_publish_date	0..1 Datetime	Date the study was first published in the AIRR Data Commons	direct
adc_update_date	0..1 Datetime	Date the study data was updated in the AIRR Data Commons	direct

Usages

used by	used in	type	used
Repertoire	study	range	Study

Identifier and Mapping Information

Schema Source

from schema: https://github.com/vdjserver/vdjserver-airr-schema

Mappings

Mapping Type	Mapped Value
self	https://github.com/vdjserver/vdjserver-airr-schema/Study
native	https://github.com/vdjserver/vdjserver-airr-schema/Study

LinkML Source

Direct

name: Study
description: Default Study description
from_schema: https://github.com/vdjserver/vdjserver-airr-schema
is_a: AIRRStandards
slots:
- study_id
- study_title
- study_type
- study_description
- inclusion_exclusion_criteria
- grants
- contributors
- pub_ids
- keywords_study
- adc_publish_date
- adc_update_date

Induced

name: Study
description: Default Study description
from_schema: https://github.com/vdjserver/vdjserver-airr-schema
is_a: AIRRStandards
attributes:
  study_id:
    name: study_id
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Unique ID assigned by study registry such as one of the International
      Nucleotide Sequence Database Collaboration (INSDC) repositories.
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Study
    domain_of:
    - Study
    - ADCDownloadCacheStudy
    - ADCDownloadCacheRepertoire
    - StatisticsCacheStudy
    - StatisticsCacheRepertoire
    range: string
  study_title:
    name: study_title
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Descriptive study title
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Study
    domain_of:
    - Study
    range: string
  study_type:
    name: study_type
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Type of study design
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    slot_uri: rdf:type
    owner: Study
    domain_of:
    - Study
    range: StudyTypeOntology
  study_description:
    name: study_description
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Generic study description
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Study
    domain_of:
    - Study
    range: string
  inclusion_exclusion_criteria:
    name: inclusion_exclusion_criteria
    annotations:
      nullable:
        tag: nullable
        value: true
    description: List of criteria for inclusion/exclusion for the study
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Study
    domain_of:
    - Study
    range: string
  grants:
    name: grants
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Funding agencies and grant numbers
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Study
    domain_of:
    - Study
    range: string
  contributors:
    name: contributors
    annotations:
      nullable:
        tag: nullable
        value: false
    description: List of individuals who contributed to the study. Note that these
      are not necessarily identical with the authors on an associated manuscript or
      other scholarly communication. Further note that typically at least the three
      CRediT contributor roles "supervision", "investigation" and "data curation"
      should be assigned. The coresponding author should be listed last.
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Study
    domain_of:
    - Study
    range: Contributor
    multivalued: true
  pub_ids:
    name: pub_ids
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Study
    domain_of:
    - GermlineSet
    - Study
    range: string
    multivalued: true
  keywords_study:
    name: keywords_study
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Keywords describing properties of one or more data sets in a study.
      "contains_schema" keywords indicate that the study contains data objects from
      the AIRR Schema of that type (Rearrangement, Clone, Cell, Receptor) while the
      other keywords indicate that the study design considers the type of data indicated
      (e.g. it is possible to have a study that "contains_paired_chain" but does not
      "contains_schema_cell").
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Study
    domain_of:
    - Study
    range: KeywordsStudyEnum
    multivalued: true
  adc_publish_date:
    name: adc_publish_date
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Date the study was first published in the AIRR Data Commons.
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Study
    domain_of:
    - Study
    range: datetime
  adc_update_date:
    name: adc_update_date
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Date the study data was updated in the AIRR Data Commons.
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: Study
    domain_of:
    - Study
    range: datetime