GA4GH SchemaBlocks - common and shared object definitions

Definition of some prototype objects which are re-used in other schema documents.

The schema definitions are done in the YAML file.

Age_class

Properties of the Age_class class

Property	Type	Format	Description
age	string		The age as ISO8601 string.
age_at_collection_class			The of the object (e.g. individual at tome of a biosample collection), as Ontology_class. object

Extended notes and examples on the Age_class properties

---

age

The age as ISO8601 string.

Example

'age' : "P56Y"

---

age_at_collection_class

The of the object (e.g. individual at tome of a biosample collection), as Ontology_class. object

Example

'age_at_collection_class' : {
  'id' : 'HP:0003621',
  'label' : 'Juvenile onset'
}

Geo_class

Properties of the Geo_class class

Property	Type	Format	Description
altitude	number	float	height in meters above the WGS 84 reference ellipsoid; otional
city	string
country	string
label	string		A text representation, preferably using standard geographic identification elements, of the corresponding latitude,longitude(,altitude). This representation serves the purposes to - capture standard data entry parameters - provide a sanity check for latitude,longitude values
latitude	number		signed decimal degrees (North, relative to Equator)
longitude	number	float	signed decimal degrees (East, relative to IERS Reference Meridian)

Extended notes and examples on the Geo_class properties

---

altitude

height in meters above the WGS 84 reference ellipsoid; otional

Example

'altitude' : 8848

---

city

Example

'city' : "Timisoara"

---

country

Example

'country' : "Romania"

---

label

A text representation, preferably using standard geographic identification elements, of the corresponding latitude,longitude(,altitude). This representation serves the purposes to

• capture standard data entry parameters
• provide a sanity check for latitude,longitude values

Example

'label' : "Str Marasesti 5, 300077 Timisoara, Romania"

---

latitude

signed decimal degrees (North, relative to Equator)

Example

'latitude' : 47.37

---

longitude

signed decimal degrees (East, relative to IERS Reference Meridian)

Example

'longitude' : 8.54

Info_class

Properties of the Info_class class

Property	Type	Format	Description
description	string		an optional free-text annotation about the object
format	string		format of the value; optional
type	string		type of the value; optional
value			the value in a format correstponding to type

Extended notes and examples on the Info_class properties

---

description

an optional free-text annotation about the object

Example

'description' : "The base length of the called segment."

---

format

format of the value; optional

Example

'format' : "int64"

---

type

type of the value; optional

Example

'type' : "number"

---

value

the value in a format correstponding to type

Example

'value' : 1503320

Ontology_class

Properties of the Ontology_class class

Property	Type	Format	Description
id	string		properly prefixed CURIE of the ontology term
label	string		the text label associated with the term

Extended notes and examples on the Ontology_class properties

---

id

properly prefixed CURIE of the ontology term

Example

'id' : "ncit:C8294"

---

label

the text label associated with the term

Example

'label' : "Pancreatic Adenocarcinoma"

Phenotype_class

Properties of the Phenotype_class class

Property	Type	Format	Description
description	string
type			the ontology term as Ontology_class
negated	boolean		Flag to indicate whether the phenotype was observed or not. Default is 'false', in other words the phenotype was observed. It is only required in cases to indicate that the phenotype was looked for, but __not__ observed.
severity			Severity of the condition e.g. subclasses of HP:0012824-Severity or SNOMED:272141005-Severities. FHIR mapping: Condition.severity
evidence	array
example

Extended notes and examples on the Phenotype_class properties

---

description

Example

'description' : ""

---

type

the ontology term as Ontology_class

Example

'type' : "undef"

---

negated

Flag to indicate whether the phenotype was observed or not. Default is ‘false’, in other words the phenotype was observed. It is only required in cases to indicate that the phenotype was looked for, but not observed.

Example

'negated' : ""

---

severity

Severity of the condition e.g. subclasses of HP:0012824-Severity or SNOMED:272141005-Severities. FHIR mapping: Condition.severity

Example

'severity' : {
  'id' : '',
  'label' : ''
}

---

evidence

Example

'evidence' : [
  {
    'id' : '',
    'label' : ''
  }
]

---

example

Example

'example' : "undef"

Reference_class

Properties of the Reference_class class

Property	Type	Format	Description
description	string
relation	string		the relation of the external reference to the object it was pointed from
type			A properly prefixed CURIE of the external reference and an associated label, represented as Ontology_class object.

Extended notes and examples on the Reference_class properties

---

description

Example

'description' : ""

---

relation

the relation of the external reference to the object it was pointed from

Example

'relation' : "denotes"

---

type

A properly prefixed CURIE of the external reference and an associated label, represented as Ontology_class object.

Example

'type' : {
  'label' : 'arrayMap 2014 ',
  'id' : 'pubmed:25428357'
}