https://raw.githubusercontent.com/EbiEga/ega-metadata-schema/main/schemas/EGA.assay.jsonMetadata schema used by the European Genome-phenome Archive (EGA) to validate its assay metadata object. This object is intended to contain metadata about the raw qualitative or quantitative test performed to determine any kind of biological property of a biological sample. It can be of different types: (1) sequencing assay [EFO:0003740] (e.g. sequence CRAM or FastQ files); and an (2) array assay [EFO:0002696] (e.g. intensity CEL files). Further details can be found in the EGA-metadata-schema GitHub repository (https://github.com/EbiEga/ega-metadata-schema/tree/main/schemas) and EGA-archive website (https://ega-archive.org/)
| Abstract | Extensible | Status | Identifiable | Custom Properties | Additional Properties | Access Restrictions | Defined In |
|---|---|---|---|---|---|---|---|
| Can be instantiated | No | Unknown status | No | Forbidden | Forbidden | none | EGA.assay.json |
object (EGA assay metadata schema)
all of
| Property | Type | Required | Nullable | Defined by |
|---|---|---|---|---|
| objectId | Merged | Required | cannot be null | EGA assay metadata schema |
| schemaDescriptor | object |
Optional | cannot be null | EGA assay metadata schema |
| objectTitle | string |
Optional | cannot be null | EGA assay metadata schema |
| objectDescription | string |
Optional | cannot be null | EGA assay metadata schema |
| assayCenter | string |
Optional | cannot be null | EGA assay metadata schema |
| assayDate | string |
Optional | cannot be null | EGA assay metadata schema |
| assayTypeSpecifications | Merged | Required | cannot be null | EGA assay metadata schema |
| assayRelationships | array |
Optional | cannot be null | EGA assay metadata schema |
| assayFiles | array |
Required | cannot be null | EGA assay metadata schema |
| assayAttributes | array |
Optional | cannot be null | EGA assay metadata schema |
Node containing the main identifiers of the object (e.g. alias, centerName...), inherited from the common definitions. #! We extend the core object (objectCoreId) by adding a pattern check based on this schema's nature: an assay (by using EGAAssayIdPattern)
objectId
-
is required
-
Type:
object(Object's IDs block) -
cannot be null
-
defined in: EGA assay metadata schema
object (Object's IDs block)
all of
-
any of
This node is intended to be used to describe the schemas and standards that a JSON document was based on. For instance, if a sample.json document was created to be validated against EGA.sample.json schema version 1.0.0, such information should be reflected in this block. This way, both a human and a machine can interpret and validate the JSON document efficiently, without the need of guessing versions.
schemaDescriptor
-
is optional
-
Type:
object(Schema descriptor) -
cannot be null
-
defined in: EGA assay metadata schema
object (Schema descriptor)
An informative assay title that should serve as an overview of the assay and differentiate it from others. This short text can be used to call out assay records in searches or in displays.
objectTitle
-
is optional
-
Type:
string(Title of the assay) -
cannot be null
-
defined in: EGA assay metadata schema
string (Title of the assay)
minimum length: the minimum number of characters for this string is: 1
"Ilumina sequencing assay 3409 - Cancer genomics"An in-depth description (e.g. used technology, sample groups, purpose...) of the assay.
objectDescription
-
is optional
-
Type:
string(Description of the assay) -
cannot be null
-
defined in: EGA assay metadata schema
string (Description of the assay)
minimum length: the minimum number of characters for this string is: 1
"Sequencing assay number 3409 of 4000. Sequenced through Illumina MiSeq to find SNPs of colorectal cancer samples..."The name of the center (e.g. 'EBI-TEST') responsible for performing assay, if applicable, in case it's different from the center submitting metadata).
assayCenter
-
is optional
-
Type:
string(Centername that performed the assay) -
cannot be null
-
defined in: EGA assay metadata schema
string (Centername that performed the assay)
minimum length: the minimum number of characters for this string is: 1
"EBI-TEST"Date when the sequencing assay took place (e.g. '2021-05-15'). If the protocols are too long, the date shall be the day the assay concluded.
assayDate
-
is optional
-
Type:
string(Date of the assay) -
cannot be null
-
defined in: EGA assay metadata schema
string (Date of the assay)
date: the string must be a date string, according to RFC 3339, section 5.6
"2021-04-30""2020-12-29"Node containing different sets of fields that depend on the instrument used for the assay: either array assays (those in which an array instrument [EFO:0002698] was used) or sequencing assays (those in which a sequencing instrument [EFO:0003739] was used). Depending on the used technology, different types of fields will be required. For example, if an array was used, its arraySampleLabels will be expected. Having this modular assay type-related node allows for easy additions of new technology-specific requirements.
assayTypeSpecifications
-
is required
-
Type:
object(Assay type specifications) -
cannot be null
-
defined in: EGA assay metadata schema
object (Assay type specifications)
all of
Comprises metadata (e.g. Source or Target) of a directional association between two entities, one of which shall be the current assay.
assayRelationships
-
is optional
-
Type: an array of merged types (Details)
-
cannot be null
-
defined in: EGA assay metadata schema
an array of merged types (Details)
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.
This property contains the specific files (e.g. raw CRAM files) derived from performing the sequencing or hybridization and scanning with the sampled material.
assayFiles
-
is required
-
Type: an array of merged types (Details)
-
cannot be null
-
defined in: EGA assay metadata schema
an array of merged types (Details)
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.
Custom attributes of an assay: reusable attributes to encode tag-value pairs (e.g. Tag being 'additional context' and its Value 'this specific assay was stored mistakenly for longer periods of time, so its data could be misleading...') with optional units. Its properties are inherited from the common-definitions.json schema.
assayAttributes
-
is optional
-
Type:
object[](Custom attribute of an object) -
cannot be null
-
defined in: EGA assay metadata schema
object[] (Custom attribute of an object)
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.