All In One Example
Below you’ll find an example of a basic submission that:
- Is attached to a collection named “blueprint”
- Has a root section with a single file, a files table and a single link attached to it
- Some of the attributes in the root section have name and value attributes
- Has a sections table
- Has a subsection with a links table
TSV
Submission S-IHECRE00000919.1
Title venous blood, Monocyte
ReleaseDate 2016-06-07
RootPath S-IHECRE00000919.1
DataSource BLUEPRINT
AttachTo blueprint
Study SECT-001
Title venous blood, Monocyte
Project CEEHRC (McGill)
Status Incomplete
Organism Homo sapiens
Tissue type venous blood
[Ontology] UBERON
(Tissue) Blood
Donor ID McGill0139
Biomaterial Type primary cells
Cell Type Monocyte
[Ontology] CL
Disease Systemic Lupus Erythematosus
[Ontology] EFO
Experiment type Single donor
File plates/J_Sero_plate_keys.xlsx
Description Summary data
Type XLSX File
Files Description Type
plates/J_Sero_plate_keys.xlsx Summary data Library File
plates/Plate01.csv Data for Plate 01 Plate Details File
Link IHECRE00000919.1
Type EpiRR
Data[SECT-001] Title Description
DT-1 Group 1 Transcription Data The data for zygotic transcription in mammals group 1
DT-2 Group 2 Transcription Data The data for zygotic transcription in mammals group 2
Stranded Total RNA-Seq SUBSECT-001 SECT-001
Links Type Assay type Experiment type Primary id
EGAD00001001282 EGA RNA-Seq Stranded Total RNA-Seq EGAX00001273202
EGAD00001001283 EGA RNA-Seq Stranded Total RNA-Seq EGAX00001273203
JSON
{
"accno": "S-IHECRE00000919.1",
"attributes": [{
"name": "RootPath",
"value": "S-IHECRE00000919.1"
}, {
"name": "Title",
"value": "venous blood, Monocyte"
}, {
"name": "ReleaseDate",
"value": "2016-06-07"
}, {
"name": "DataSource",
"value": "BLUEPRINT"
}, {
"name": "AttachTo",
"value": "blueprint"
}],
"section": {
"accno": "SECT-001",
"attributes": [{
"name": "Title",
"value": "venous blood, Monocyte"
}, {
"name": "Project",
"value": "CEEHRC (McGill)"
}, {
"name": "Status",
"value": "Incomplete"
}, {
"name": "Organism",
"value": "Homo sapiens"
}, {
"name": "Tissue type",
"value": "venous blood",
"nmqual": [{
"name": "Tissue",
"value": "Blood"
}],
"valqual": [{
"name": "Ontology",
"value": "UBERON"
}]
}, {
"name": "Donor ID",
"value": "McGill0139"
}, {
"name": "Biomaterial Type",
"value": "primary cells"
}, {
"name": "Cell Type",
"value": "Monocyte",
"valqual": [{
"name": "Ontology",
"value": "CL"
}]
}, {
"name": "Disease",
"value": "Systemic Lupus Erythematosus",
"valqual": [{
"name": "Ontology",
"value": "EFO"
}]
}, {
"name": "Experiment type",
"value": "Single donor"
}],
"files": [{
"path": "plates/J_Sero_plate_keys.xlsx",
"attributes": [{
"name": "Description",
"value": "Summary data"
}, {
"name": "Type",
"value": "XLSX File"
}]
}, [{
"path": "plates/J_Sero_plate_keys.xlsx",
"attributes": [{
"name": "Description",
"value": "Summary data"
}, {
"name": "Type",
"value": "Library File"
}]
}, {
"path": "plates/Plate01.csv",
"attributes": [{
"name": "Description",
"value": "Data for Plate 01"
}, {
"name": "Type",
"value": "Plate Details File"
}]
}]],
"links": [{
"url": "IHECRE00000919.1",
"attributes": [{
"name": "Type",
"value": "EpiRR"
}]
}],
"subsections": [{
"accno": "SUBSECT-001",
"links": [[{
"url": "EGAD00001001282",
"attributes": [{
"name": "Type",
"value": "EGA"
}, {
"name": "Assay type",
"value": "RNA-Seq"
}, {
"name": "Experiment type",
"value": "Stranded Total RNA-Seq"
}, {
"name": "Primary id",
"value": "EGAX00001273202"
}]
}, {
"url": "EGAD00001001283",
"attributes": [{
"name": "Type",
"value": "EGA"
}, {
"name": "Assay type",
"value": "RNA-Seq"
}, {
"name": "Experiment type",
"value": "Stranded Total RNA-Seq"
}, {
"name": "Primary id",
"value": "EGAX00001273203"
}]
}]],
"type": "Stranded Total RNA-Seq"
}, [{
"accno": "DT-1",
"attributes": [{
"name": "Title",
"value": "Group 1 Transcription Data"
}, {
"name": "Description",
"value": "The data for zygotic transcription in mammals group 1"
}],
"type": "Data"
}, {
"accno": "DT-2",
"attributes": [{
"name": "Title",
"value": "Group 2 Transcription Data"
}, {
"name": "Description",
"value": "The data for zygotic transcription in mammals group 2"
}],
"type": "Data"
}]],
"type": "Study"
},
"type": "submission"
}