Proposed Schemas with Value Domains Specified
- Nicole Deflaux (Unlicensed)
Owned by Nicole Deflaux (Unlicensed)
Introduction
Now that users are going to start putting data into the system, we need a way to communicate to them what values are manditory, optional, and what value domains are allowed. Please add your thoughts to this wiki page as the month progresses and we work with our Scientists.
JSON Schema
The JsonSchema is an emerging standard similar to DTDs for XML.
See type descriptors here http://tools.ietf.org/html/draft-zyp-json-schema-03#section-5
Query Results Schema
{
"properties": {
"results": {
"items": {"type": "object"},
"type": "array"
},
"totalNumberOfResults": {"type": "number"}
},
"type": "object"
}
Project Schema
The JsonSchema is an emerging standard similar to DTDs for XML.
{
"properties": {
"accessControlList": {"type": "string"},
"annotations": {"type": "string"},
"creationDate": {"type": "number"},
"creator": {"type": "string"},
"description": {"type": "string"},
"etag": {"type": "string"},
"id": {"type": "string"},
"name": {"type": "string"},
"parentId": {"type": "string"},
"uri": {"type": "string"}
},
"type": "object"
}
'creator' needs to be changed to 'createdBy' so that we can query upon it
Dataset Schema
The JsonSchema is an emerging standard similar to DTDs for XML.
{
"properties": {
"accessControlList": {"type": "string"},
"annotations": {"type": "string"},
"creationDate": {"type": "number"},
"creator": {"type": "string"},
"description": {"type": "string"},
"etag": {"type": "string"},
"hasClinicalData": {"type": "boolean"},
"hasExpressionData": {"type": "boolean"},
"hasGeneticData": {"type": "boolean"},
"id": {"type": "string"},
"layers": {"type": "string"},
"locations": {"type": "string"},
"name": {"type": "string"},
"parentId": {"type": "string"},
"releaseDate": {"type": "number"},
"status": {"type": "string"},
"uri": {"type": "string"},
"version": {"type": "string"}
},
"type": "object"
}
'creator' needs to be changed to 'createdBy' so that we can query upon it
Layer Schema
The JsonSchema is an emerging standard similar to DTDs for XML.
{
"properties": {
"accessControlList": {
"description": "the uri to access the ACL for this
Layer",
"type": "string",
"format": "uri",
},
"annotations": {
"description": "SYSTEM CONTROLLED, the uri to access the annotations for
this Layer",
"type": "string",
"format": "uri",
},
"creationDate": {
"description": "SYSTEM CONTROLLED, the creation date of this metadata in
Synapse",
"type": "integer",
"format": "utc-millisec",
},
"description": {
"description": "a narrative blurb of text about this layer",
"type": "string",
"format": "text"
},
"etag": {
"description": "SYSTEM CONTROLLED, a value used for optimistic
concurrency control as a way to help prevent simultaneous
updates of a resource from overwriting each other",
"type": "string",
},
"id": {
"description": "SYSTEM CONTROLLED, the Synapse identifier for this entity",
"type": "string",
"format": "text",
},
"locations": {
"description": "SYSTEM CONTROLLED, the uri to access the location metadata
regarding where the data for this layer is actually stored",
"type": "string",
"format": "uri",
},
"name": {
"description": "the display name of this layer",
"type": "string",
"format": "text",
"required": true
},
"numSamples": {
"description": "the number of samples in this layer",
"type": "integer",
"minimum": 0
},
"parentId": {
"description": "the Synapse identifier for this entity, all
layers must have a parent",
"type": "string",
"format": "text",
"required": true,
},
"platform": {
"description": "the platform upon which the samples were
processed (primary ontology: Ontology Of
Biomedical Investigation)",
"type": "string",
"format": ["ontology:OBI", "ontology:SageBioCustom"]
},
"previews": {
"description": "SYSTEM CONTROLLED, the uri to access the previews for
this Layer",
"type": "string",
"format": "uri",
},
"processingFacility": {
"description": "the ontological term best-fitting
the facility in which this data was
processed, (primary ontology:
Ontology Of Biomedical
Investigation)",
"type": "string",
"format": ["ontology:OBI", "ontology:SageBioCustom"]
},
"publicationDate": {
"description": "the publication date of the notable
paper for the data in this layer",
"type": "integer",
"format": "utc-millisec"
},
"qcBy": {
"description": "the Synapse username of the person who QCed this
layer",
"type": "string",
"format": "text"
},
"qcDate": {
"description": "the date upon which this Layer was QCed",
"type": "number",
"format": "utc-millisec"
},
"releaseNotes": {
"description": "free text regarding any release notes
associated with this layer",
"type": "string",
"format": "text"
},
"status": {
"type": "string",
"enum": ["QCed", "Curated", "Raw", "Unknown"],
"default": "Uknown"
},
"tissueType": {
"description": "the ontological term best-fitting the
tissue type found in this layer,
(primary ontology: Foundational Model Of Anatomy)",
"type": "string",
"format": ["ontology:FMA", "ontology:SageBioCustom"]
},
"type": {
"description": "the high-level type of data this layer holds",
"type": "string",
"enum": ["C", "E", "G"],
"required": true
},
"uri": {
"uri": "SYSTEM CONTROLLED, the uri to access this Layer",
"type": "string",
"format": "uri",
},
"version": {
"description": "the Synapse version of this Layer",
"type": "string",
"pattern": "^\d+\.\d+\.\d+$",
}
},
"type": "object"
}
More suggestions:
- Xa: Layers should list both who did the curation and who did the QC, and on what date. Right now this info resided in the dataset but different folks might curate different layers. More: we should say "processedBy" and agree that for all data we will have a curated layer, qced layer, etc... and use references to refer to the layer that was input to the process step.
- Matt: We also need a new field for "platformVendor", but this value should come from a controlled vocabulary. (The analogy here is that this is the make of the car.) This set should include:
- Affymetrix
- Agillent
- Illumina
- Perligen
- Nimblegen
- Custom
- Matt: We also need to think more carefully about the values we are using for "platform". BioConductor has a list of these that we might use as our controlled vocabulary. (The analogy here is that this is the model of the car.)
- Adam: nothing should be called "clinical" layer or "C" since that is too specific. It should be "phenotypic" layer or "P".
Layer Preview Schema
The JsonSchema is an emerging standard similar to DTDs for XML.
{
"properties": {
"accessControlList": {"type": "string"},
"annotations": {"type": "string"},
"creationDate": {"type": "number"},
"etag": {"type": "string"},
"headers": {
"items": {"type": "string"},
"type": "array"
},
"id": {"type": "string"},
"name": {"type": "string"},
"parentId": {"type": "string"},
"previewBlob": {
"items": {"type": "string"},
"type": "array"
},
"previewString": {"type": "string"},
"rows": {
"items": {"type": "object"},
"type": "array"
},
"uri": {"type": "string"}
},
"type": "object"
}
Dataset or Layer Locations Schema
The JsonSchema is an emerging standard similar to DTDs for XML.
{
"properties": {
"accessControlList": {"type": "string"},
"annotations": {"type": "string"},
"creationDate": {"type": "number"},
"etag": {"type": "string"},
"id": {"type": "string"},
"md5sum": {"type": "string"},
"name": {"type": "string"},
"parentId": {"type": "string"},
"path": {"type": "string"},
"type": {"type": "string"},
"uri": {"type": "string"}
},
"type": "object"
}
Annotations Schema
The JsonSchema is an emerging standard similar to DTDs for XML.
{
"properties": {
"blobAnnotations": {"type": "object"},
"creationDate": {"type": "number"},
"dateAnnotations": {"type": "object"},
"doubleAnnotations": {"type": "object"},
"etag": {"type": "string"},
"id": {"type": "string"},
"longAnnotations": {"type": "object"},
"stringAnnotations": {"type": "object"},
"uri": {"type": "string"}
},
"type": "object"
}
Access Control List Schema
The JsonSchema is an emerging standard similar to DTDs for XML.
{
"properties": {
"createdBy": {"type": "string"},
"creationDate": {"type": "number"},
"etag": {"type": "string"},
"id": {"type": "string"},
"modifiedBy": {"type": "string"},
"modifiedOn": {"type": "number"},
"resourceAccess": {
"items": {
"properties": {
"accessType": {
"items": {"type": "string"},
"type": "array"
},
"id": {"type": "string"},
"userGroupId": {"type": "string"}
},
"type": "object"
},
"type": "array"
},
"resourceId": {"type": "string"},
"uri": {"type": "string"}
},
"type": "object"
}