Class: Participant

Table containing participant information

classDiagram class Participant click Participant href "../Participant" Participant : affected_status Participant --> "1" AffectedStatusEnum : affected_status click AffectedStatusEnum href "../AffectedStatusEnum" Participant : age_at_enrollment Participant : age_at_last_observation Participant : ancestry_detail Participant : consent_code Participant --> "1" ConsentCodeEnum : consent_code click ConsentCodeEnum href "../ConsentCodeEnum" Participant : family_id Participant : gregor_center Participant --> "1" GregorCenterEnum : gregor_center click GregorCenterEnum href "../GregorCenterEnum" Participant : internal_project_id Participant : maternal_id Participant : missing_variant_case Participant --> "1" MissingVariantCaseEnum : missing_variant_case click MissingVariantCaseEnum href "../MissingVariantCaseEnum" Participant : missing_variant_details Participant : participant_id Participant : paternal_id Participant : phenotype_description Participant : pmid_id Participant : prior_testing Participant : proband_relationship Participant --> "1" ProbandRelationshipEnum : proband_relationship click ProbandRelationshipEnum href "../ProbandRelationshipEnum" Participant : proband_relationship_detail Participant : recontactable Participant --> "0..1" RecontactableEnum : recontactable click RecontactableEnum href "../RecontactableEnum" Participant : reported_ethnicity Participant --> "0..1" ReportedEthnicityEnum : reported_ethnicity click ReportedEthnicityEnum href "../ReportedEthnicityEnum" Participant : reported_race Participant --> "*" ReportedRaceEnum : reported_race click ReportedRaceEnum href "../ReportedRaceEnum" Participant : sex Participant --> "1" SexEnum : sex click SexEnum href "../SexEnum" Participant : sex_detail Participant : solve_status Participant --> "1" SolveStatusEnum : solve_status click SolveStatusEnum href "../SolveStatusEnum" Participant : twin_id

Slots

Name	Cardinality and Range	Description	Inheritance
participant_id	1 String		direct
internal_project_id	* String	An identifier used by GREGoR research centers to identify a set of participan...	direct
gregor_center	1 GregorCenterEnum	GREGoR Center to which the participant is originally associated	direct
consent_code	1 ConsentCodeEnum	Consent group pertaining to this participant's data	direct
recontactable	0..1 RecontactableEnum	Is the originating GREGoR Center likely able to recontact this participant	direct
prior_testing	* String	Text description of any genetic testing for individual conducted prior to enr...	direct
pmid_id	* String	Case specific PubMed ID if applicable	direct
family_id	1 String	Identifier for family (primary key)	direct
paternal_id	1 String	participant_id for father; 0 if not available	direct
maternal_id	1 String	participant_id for mother; 0 if not available	direct
twin_id	* String	participant_id for twins, triplets, etc; 0 if not available	direct
proband_relationship	1 ProbandRelationshipEnum	Text description of individual relationship to proband in family, especially ...	direct
proband_relationship_detail	0..1 String	Other proband relationship not captured in enumeration above	direct
sex	1 SexEnum	Biological sex assigned at birth (aligned with All of Us)	direct
sex_detail	0..1 String	Optional free-text field to describe known discrepancies between 'sex' value ...	direct
reported_race	* ReportedRaceEnum	Self/submitter-reported race (OMB categories)	direct
reported_ethnicity	0..1 ReportedEthnicityEnum	Self/submitter-reported ethnicity (OMB categories)	direct
ancestry_detail	0..1 String	Additional specific ancestry description free text beyond what is captured by...	direct
age_at_last_observation	0..1 Float	Age at last observation, aka age in years at the last time the center can vou...	direct
affected_status	1 AffectedStatusEnum	Indicate affected status of individual (overall with respect to primary pheno...	direct
phenotype_description	* String	human-readable 'Phenotypic one-line summary' for why this individual is of in...	direct
age_at_enrollment	0..1 Float	age in years at which consent was originally obtained	direct
solve_status	1 SolveStatusEnum	Indication of whether the submitting RC considers this case 'solved'	direct
missing_variant_case	1 MissingVariantCaseEnum	Indication of whether this is known to be a missing variant case, see notes f...	direct
missing_variant_details	0..1 String	For missing variant cases, indicate gene(s) or region of interest and reason ...	direct

Identifier and Mapping Information

Schema Source

from schema: https://w3id.org/madanucd/gregor_linkml

Mappings

Mapping Type	Mapped Value
self	gregor_linkml:Participant
native	gregor_linkml:Participant

LinkML Source

Direct

name: Participant
description: Table containing participant information
from_schema: https://w3id.org/madanucd/gregor_linkml
slots:
- participant_id
- internal_project_id
- gregor_center
- consent_code
- recontactable
- prior_testing
- pmid_id
- family_id
- paternal_id
- maternal_id
- twin_id
- proband_relationship
- proband_relationship_detail
- sex
- sex_detail
- reported_race
- reported_ethnicity
- ancestry_detail
- age_at_last_observation
- affected_status
- phenotype_description
- age_at_enrollment
- solve_status
- missing_variant_case
- missing_variant_details

Induced

name: Participant
description: Table containing participant information
from_schema: https://w3id.org/madanucd/gregor_linkml
attributes:
  participant_id:
    name: participant_id
    description: ''
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: participant_id
    owner: Participant
    domain_of:
    - Participant
    - Phenotype
    - Genetic_findings
    - Analyte
    - Experiment
    - Aligned
    range: string
    required: true
  internal_project_id:
    name: internal_project_id
    description: An identifier used by GREGoR research centers to identify a set of
      participants for their internal tracking
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    multivalued: true
    alias: internal_project_id
    owner: Participant
    domain_of:
    - Participant
    range: string
  gregor_center:
    name: gregor_center
    description: GREGoR Center to which the participant is originally associated
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: gregor_center
    owner: Participant
    domain_of:
    - Participant
    range: Gregor_centerEnum
    required: true
  consent_code:
    name: consent_code
    description: Consent group pertaining to this participant's data
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: consent_code
    owner: Participant
    domain_of:
    - Participant
    range: Consent_codeEnum
    required: true
  recontactable:
    name: recontactable
    description: Is the originating GREGoR Center likely able to recontact this participant
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: recontactable
    owner: Participant
    domain_of:
    - Participant
    range: RecontactableEnum
  prior_testing:
    name: prior_testing
    description: Text description of any genetic testing for individual conducted
      prior to enrollment
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    multivalued: true
    alias: prior_testing
    owner: Participant
    domain_of:
    - Participant
    range: string
  pmid_id:
    name: pmid_id
    description: Case specific PubMed ID if applicable
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    multivalued: true
    alias: pmid_id
    owner: Participant
    domain_of:
    - Participant
    range: string
  family_id:
    name: family_id
    description: Identifier for family (primary key)
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    identifier: true
    alias: family_id
    owner: Participant
    domain_of:
    - Participant
    - Family
    range: string
    required: true
  paternal_id:
    name: paternal_id
    description: participant_id for father; 0 if not available
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: paternal_id
    owner: Participant
    domain_of:
    - Participant
    range: string
    required: true
  maternal_id:
    name: maternal_id
    description: participant_id for mother; 0 if not available
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: maternal_id
    owner: Participant
    domain_of:
    - Participant
    range: string
    required: true
  twin_id:
    name: twin_id
    description: participant_id for twins, triplets, etc; 0 if not available
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    multivalued: true
    alias: twin_id
    owner: Participant
    domain_of:
    - Participant
    range: string
  proband_relationship:
    name: proband_relationship
    description: Text description of individual relationship to proband in family,
      especially useful to capture relationships when connecting distant relatives
      and connecting relatives not studied
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: proband_relationship
    owner: Participant
    domain_of:
    - Participant
    range: Proband_relationshipEnum
    required: true
  proband_relationship_detail:
    name: proband_relationship_detail
    description: Other proband relationship not captured in enumeration above
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: proband_relationship_detail
    owner: Participant
    domain_of:
    - Participant
    range: string
  sex:
    name: sex
    description: Biological sex assigned at birth (aligned with All of Us). If individual
      has a known DSD / not expected sex chromosome karyotype, this can be noted in
      the phenotype information section.
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: sex
    owner: Participant
    domain_of:
    - Participant
    range: SexEnum
    required: true
  sex_detail:
    name: sex_detail
    description: Optional free-text field to describe known discrepancies between
      'sex' value (female=>XX, male=>XY) and actual sex chromosome karyotype
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: sex_detail
    owner: Participant
    domain_of:
    - Participant
    range: string
  reported_race:
    name: reported_race
    description: Self/submitter-reported race (OMB categories)
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    multivalued: true
    alias: reported_race
    owner: Participant
    domain_of:
    - Participant
    range: Reported_raceEnum
  reported_ethnicity:
    name: reported_ethnicity
    description: Self/submitter-reported ethnicity (OMB categories)
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: reported_ethnicity
    owner: Participant
    domain_of:
    - Participant
    range: Reported_ethnicityEnum
  ancestry_detail:
    name: ancestry_detail
    description: Additional specific ancestry description free text beyond what is
      captured by OMB race/ethnicity categories
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: ancestry_detail
    owner: Participant
    domain_of:
    - Participant
    range: string
  age_at_last_observation:
    name: age_at_last_observation
    description: Age at last observation, aka age in years at the last time the center
      can vouch for the accuracy phenotype data. For conditions with later age of
      onset, this field lets users know if individuals marked as unaffected were younger
      or older than the age when the phenotype is expected to appear.
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: age_at_last_observation
    owner: Participant
    domain_of:
    - Participant
    range: float
  affected_status:
    name: affected_status
    description: 'Indicate affected status of individual (overall with respect to
      primary phenotype in the family). Note: Affected participants must have entry
      in phenotype table.'
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: affected_status
    owner: Participant
    domain_of:
    - Participant
    range: Affected_statusEnum
    required: true
  phenotype_description:
    name: phenotype_description
    description: human-readable 'Phenotypic one-line summary' for why this individual
      is of interest. Could be the same as the term_details value in the Phenotype
      table. Strongly encourage/required for proband.
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    multivalued: true
    alias: phenotype_description
    owner: Participant
    domain_of:
    - Participant
    range: string
  age_at_enrollment:
    name: age_at_enrollment
    description: age in years at which consent was originally obtained
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: age_at_enrollment
    owner: Participant
    domain_of:
    - Participant
    range: float
  solve_status:
    name: solve_status
    description: Indication of whether the submitting RC considers this case 'solved'
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: solve_status
    owner: Participant
    domain_of:
    - Participant
    range: Solve_statusEnum
    required: true
  missing_variant_case:
    name: missing_variant_case
    description: Indication of whether this is known to be a missing variant case,
      see notes for a description of the Missing Variant Project and inclusion criteria.
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: missing_variant_case
    owner: Participant
    domain_of:
    - Participant
    range: Missing_variant_caseEnum
    required: true
  missing_variant_details:
    name: missing_variant_details
    description: For missing variant cases, indicate gene(s) or region of interest
      and reason for inclusion in MVP.
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: missing_variant_details
    owner: Participant
    domain_of:
    - Participant
    range: string