mSCAPE Downstream Analyses Specification

A downstream analysis is a record of a pipeline run carried out on data already held in Onyx. It is a distinct object type from a project record: an analysis describes how a result was produced (pipeline, version, command, methods) and what it produced (result, metrics, report, outputs), and links back to the project records it was produced from and to any upstream analyses it was derived from.

Analyses are identified by an analysis_id of the form A-XXXXXXXXXX, assigned automatically by Onyx on submission.

The Submission Specification below lists the fields that can be provided when creating or updating an analysis. The Read Specification lists all fields visible when retrieving an analysis, including those assigned by Onyx.

Submission Specification

Required fields

Field	Data type	Description	Restrictions
site	choice	Site that uploaded the object.	• Choices: barts, bham, cuh, gosh, gstt, hpruphg, nuth, public, ripl, ucl, uclh, uhl, uhs, ukhsa, ukhsabris, ukhsamanc, wtsi
analysis_date	date	The date the analysis was carried out.	• Input formats: iso-8601 • Output format: iso-8601
name	text	Name for the analysis, unique to the project.	• Max length: 50
pipeline_name	text	Name of the pipeline used for the analysis.	• Max length: 50
pipeline_version	text	Version of the pipeline used for the analysis.	• Max length: 10
result	text	Key findings of the analysis.	• Max length: 200
identifiers	identifiers	Key anonymised identifiers involved in the analysis. This does not include the CLIMB ID (for these, see the {project}_records field).

Optional fields

Field	Data type	Description	Restrictions
is_published	bool	Indicator for whether an object has been published.	• Default: True
description	text	Description of the analysis.	• Max length: 500
pipeline_url	text	URL to the pipeline used for the analysis.	• Max length: 200
pipeline_command	text	Command used to run the pipeline for the analysis.	• Max length: 200
methods	structure	Structured details of the experiment run and its inputs.	• Default: {}
result_metrics	structure	Structured output metrics from the result of the analysis.	• Default: {}
report	text	HTML report produced from the analysis.	• Max length: 200
outputs	text	Directory of outputs produced from the analysis.	• Max length: 200
upstream_analyses	identifiers	The analyses that this analysis depends on.
mscape_records	identifiers	The records this analysis was produced from.

Read Specification

Fields

Field	Data type	Description	Restrictions
published_date	date	The date the object was published in Onyx.	• Output format: iso-8601
site	choice	Site that uploaded the object.	• Choices: barts, bham, cuh, gosh, gstt, hpruphg, nuth, public, ripl, ucl, uclh, uhl, uhs, ukhsa, ukhsabris, ukhsamanc, wtsi
analysis_id	text	Unique identifier for an analysis in Onyx.
analysis_date	date	The date the analysis was carried out.	• Output format: iso-8601
name	text	Name for the analysis, unique to the project.
description	text	Description of the analysis.
pipeline_name	text	Name of the pipeline used for the analysis.
pipeline_url	text	URL to the pipeline used for the analysis.
pipeline_version	text	Version of the pipeline used for the analysis.
pipeline_command	text	Command used to run the pipeline for the analysis.
methods	structure	Structured details of the experiment run and its inputs.
result	text	Key findings of the analysis.
result_metrics	structure	Structured output metrics from the result of the analysis.
report	text	HTML report produced from the analysis.
outputs	text	Directory of outputs produced from the analysis.
upstream_analyses	identifiers	The analyses that this analysis depends on.
downstream_analyses	identifiers	The analyses that depend on this analysis.
identifiers	identifiers	Key anonymised identifiers involved in the analysis. This does not include the CLIMB ID (for these, see the {project}_records field).
mscape_records	identifiers	The records this analysis was produced from.