Skip to content

Latest commit

 

History

History
154 lines (88 loc) · 10.2 KB

ega-6-properties-minimal-public-attributes-describing-an-individual.md

File metadata and controls

154 lines (88 loc) · 10.2 KB

Minimal public attributes describing an individual Schema

https://raw.githubusercontent.com/EbiEga/ega-metadata-schema/main/schemas/EGA.individual.json#/properties/minimalPublicAttributes

Among all attributes describing an individual, some may contain identifiable metadata and thus must be private. Nevertheless, there are three/four required attributes (even if they are unknown): subject id, biological sex, phenotypicAbnormalities and/or diseases. These shall be displayed and queryable on our portal. In the case of a healthy individual (with no phenotypic abnormalities nor diseases), the 'phenotypicAbnormalities' and 'diseases' arrays will contain a reference to 'Unaffected' [NCIT:C94232]. Do take into account the 'excluded' property of each 'disease' or 'phenotypicAbnormality' in order to evaluate it correctly, since logic negation can be provided using that property.

Abstract Extensible Status Identifiable Custom Properties Additional Properties Access Restrictions Defined In
Can be instantiated No Unknown status No Forbidden Forbidden none EGA.individual.json*

minimalPublicAttributes Type

object (Minimal public attributes describing an individual)

any of

minimalPublicAttributes Properties

Property Type Required Nullable Defined by
subjectId string Required cannot be null EGA individual metadata schema
biologicalSex string Required cannot be null EGA individual metadata schema
phenotypicAbnormalities array Optional cannot be null EGA individual metadata schema
diseases array Optional cannot be null EGA individual metadata schema

subjectId

A unique identifier (e.g. 'Donor-10031') for the subject the sample derives from, providing context for the sample to be better understood through its provenance. It shall not contain personal sensitive data, since it will be publicly displayed for queries and searches.

subjectId

subjectId Type

string (Subject ID)

subjectId Constraints

minimum length: the minimum number of characters for this string is: 1

subjectId Examples

"Donor-10031"
"ID001"
"9001"
"AX_Dli"

biologicalSex

An organismal quality inhering in a bearer by virtue of the bearer's physical expression of sexual characteristics. In other words, the trait that determines the individual's (from which the sample derives) reproductive function: mainly male or female. Term chosen from a list of controlled vocabulary (CV). If you cannot find your term in the CV list, please create an issue at our metadata GitHub repository proposing its addition.

biologicalSex

biologicalSex Type

string (Biological sex of the individual)

biologicalSex Constraints

enum: the value of this property must be equal to one of the following values:

Value Explanation
"male" [PATO:0000384]: A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes.
"female" [PATO:0000383]: A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes.
"hermaphrodite" [PATO:0001340]: An organism having both male and female sexual characteristics and organs. A biological sex quality inhering in an organism or a population with both male and female sexual organs in one individual.
"pseudohermaphrodite" [PATO:0001827]: A biological sex quality inhering in an individual or a population by virtue of having internal reproductive organs of one sex and external sexual characteristics of the other sex.
"unknown" [NCIT:C17998]: The biological sex is unknown, not assesed or not available.

biologicalSex Examples

"male"

phenotypicAbnormalities

phenotypicAbnormalities

phenotypicAbnormalities Type

object[] (Phenotypic abnormality item)

phenotypicAbnormalities Constraints

minimum number of items: the minimum number of items for this array is: 1

unique items: all items in this array must be unique. Duplicates are not allowed.

diseases

diseases

diseases Type

object[] (Disease item)

diseases Constraints

minimum number of items: the minimum number of items for this array is: 1

unique items: all items in this array must be unique. Duplicates are not allowed.