Type: object
Description: Schema for the experimental run (e.g. sequencing run, array processing…) leading to the raw data for the (computational) analysis.

Properties

biosampleId

• type: string

Reference to the biosample ID.

biosampleId Value Example

"008dafdd-a3d1-4801-8c0a-8714e2b58e48"

id

• type: string

Run ID.

id Value Example

"SRR10903401"

individualId

• type: string

Reference to the individual ID.

individualId Value Example

"TCGA-AO-A0JJ"

info

• type: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/beaconCommonComponents.json#/definitions/Info [LINK]

libraryLayout

• type: string

Ontology value for the library layout e.g “PAIRED”, “SINGLE” #todo add Ontology name?

librarySelection

• type: string

Selection method for library preparation, e.g “RANDOM”, “RT-PCR”

librarySelection Value Examples

"RANDOM"

"RT-PCR"

librarySource

• type: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/ontologyTerm.json [LINK]

Ontology value for the source of the sequencing or hybridization library, e.g “genomic source”, “transcriptomic source”

librarySource Value Examples

{
   "id" : "GENEPIO:0001966",
   "label" : "genomic source"
}

{
   "id" : "GENEPIO:0001965",
   "label" : "metagenomic source"
}

libraryStrategy

• type: string

Library strategy, e.g. “WGS”

libraryStrategy Value Example

"WGS"

platform

• type: string

General platform technology label. It SHOULD be a subset of the platformModel and used only for query convenience, e.g. “return everything sequenced with Illimuna”, where the specific model is not relevant

platform Value Examples

"Illumina"

"Oxford Nanopore"

"Affymetrix"

platformModel

• type: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/ontologyTerm.json [LINK]

Ontology value for experimental platform or methodology used. For sequencing platforms the use of “OBI:0400103 - DNA sequencer” is suggested.

platformModel Value Examples

{
   "id" : "OBI:0002048",
   "label" : "Illumina HiSeq 3000"
}

{
   "id" : "OBI:0002750",
   "label" : "Oxford Nanopore MinION"
}

{
   "id" : "EFO:0010938",
   "label" : "large-insert clone DNA microarray"
}

runDate

• type: string (date)

Date at which the experiment was performed.

runDate Value Example

"2021-10-18"