Sequence Based Assay schema and standards

1. Measurement Set Metadata

Overview

A Measurement Set represents a distinct measurement, such as the sequencing of a genomic library generated by an experiment performed on a cell line. It contains the raw data files generated by the measurement.

Required Fields

The following fields are required when creating a Measurement Set:

• assay_term: The assay used to produce data in this measurement set
• award: Grant associated with the submission
• file_set_type: The category that best describes this measurement set (default: "experimental data")
• lab: Lab associated with the submission
• samples: The sample(s) associated with this file set (maximum of 1)

Important Rules

1. Mutually Exclusive Fields: Specification of samples is mutually exclusive with specification of donors.
2. Status Requirements:
   • Release, archived, and revoked status should have release_timestamp specified
   • Release timestamp is required if status is released, revoked, or archived

Field Descriptions

Basic Information

• accession: A unique identifier prefixed with PKB (server-assigned)
• aliases: Lab-specific identifiers to reference an object (Format: lab-name:identifier)
• description: A plain text description of the object
• file_set_type: The category of this measurement set (default: "experimental data")
• status: The status of the metadata object (admin-only, default: "in progress")
• submitter_comment: Additional information from submitter

Scientific Information

• assay_term: The assay used to produce data (links to AssayTerm)
• samples: Sample(s) associated with this file set (maximum of 1)
• donors: Donors of the samples (if not using samples; not directly submittable)
• preferred_assay_title: Custom lab preferred label for the experiment (from controlled vocabulary)
• library_construction_platform: Platform used to construct the library (links to PlatformTerm)
• sequencing_library_types: Description of libraries sequenced (from controlled list)
• donor_validation_method: Method for mapping data to donor
• multiome_size: Number of datasets in a multiome experiment (minimum: 2)
• targeted_genes: Genes targeted in this assay (maximum: 100)

Related Data

• control_file_sets: File sets as scientific controls
• auxiliary_sets: Auxiliary sets of files produced alongside raw data
• files: Files associated with this file set (not directly submittable)
• control_for: File sets for which this is a control (not directly submittable)
• input_file_set_for: File sets that use this as input (not directly submittable)
• related_multiome_datasets: Related datasets in the multiome experiment (not directly submittable)

References

• dbxrefs: External resource identifiers (Pattern: ^GEO:GSE\d+$)
• documents: Documents providing additional information (links to Document)
• publication_identifiers: Publication identifiers (various formats accepted)
• protocols: Links to protocols for conducting the assay
• external_image_url: Links to external image storage (URL format)

Administrative Fields

• award: Grant associated with the submission (links to Award)
• lab: Lab associated with the submission (links to Lab)
• uuid: Unique identifier for the object (server-assigned)
• collections: Data collections the samples are part of (admin-only)
• schema_version: JSON schema version (default: "17")
• alternate_accessions: Previous accessions for merged objects (admin-only)
• creation_timestamp: Object creation date (server-assigned)
• release_timestamp: Object release date (admin-only)
• submitted_by: User who submitted the object (server-assigned)
• submitted_files_timestamp: Timestamp of first file creation (not submittable)
• notes: DACC internal notes (admin-only)
• revoke_detail: Explanation for revoked status (admin-only)

2. Analysis Set Metadata

a) Intermediate Analysis Set

b) Principal Analysis Set

Overview

An Analysis Set represents the results of a computational analysis of raw genomic data or other analyses. Analysis sets can be either intermediate (part of a larger analysis chain) or principal (final interpretable results).

Required Fields

The following fields are required when creating an Analysis Set:

• award: Grant associated with the submission
• file_set_type: The level of this analysis set ("intermediate analysis" or "principal analysis")
• lab: Lab associated with the submission

Additionally, input_file_sets is required if the file_set_type is "principal analysis".

Important Rules

1. Mutually Exclusive Fields: Specification of samples is mutually exclusive with specification of donors.
2. Status Requirements:
   • Release, archived, and revoked status should have release_timestamp specified
   • Release timestamp is required if status is released, revoked, or archived
3. Principal Analysis Requirement:
   • If file_set_type is "principal analysis", then input_file_sets must be specified

Field Descriptions

Basic Information

• accession: A unique identifier prefixed with PKB (server-assigned)
• aliases: Lab-specific identifiers to reference an object (Format: lab-name:identifier)
• description: A plain text description of the object
• file_set_type: The level of this analysis set ("intermediate analysis" or "principal analysis")
• status: The status of the metadata object (admin-only, default: "in progress")
• submitter_comment: Additional information from submitter

Analysis Information

• input_file_sets: File set(s) required for this analysis (required for principal analysis)
• samples: Sample(s) associated with this file set (mutually exclusive with donors)
• donors: Donors of the samples (not directly submittable)
• assay_titles: Titles of assays that produced data analyzed (not directly submittable)

Related Data

• files: Files associated with this file set (not directly submittable)
• control_for: File sets for which this is a control (not directly submittable)
• input_file_set_for: File sets that use this as input (not directly submittable)

References

• dbxrefs: External resource identifiers (Pattern: ^GEO:GSE\d+$)
• documents: Documents providing additional information (links to Document)
• publication_identifiers: Publication identifiers (various formats accepted)

Administrative Fields

• award: Grant associated with the submission (links to Award)
• lab: Lab associated with the submission (links to Lab)
• uuid: Unique identifier for the object (server-assigned)
• collections: Data collections the samples are part of (admin-only)
• schema_version: JSON schema version (default: "7")
• alternate_accessions: Previous accessions for merged objects (admin-only)
• creation_timestamp: Object creation date (server-assigned)
• release_timestamp: Object release date (admin-only)
• submitted_by: User who submitted the object (server-assigned)
• submitted_files_timestamp: Timestamp of first file creation (not submittable)
• notes: DACC internal notes (admin-only)
• revoke_detail: Explanation for revoked status (admin-only)

Types of Analysis Sets

Intermediate Analysis

• Processed data which are not the final results of an experiment
• May not be interpretable on their own
• Part of a larger analysis pipeline

Principal Analysis

• Processed data which are the final results of an experiment
• Results can be interpretable on their own
• Requires specification of input_file_sets

Relationship with Measurement Sets

Analysis Sets often process data from Measurement Sets. The connection is made through the input_file_sets field, which can reference Measurement Sets or other Analysis Sets that served as input for the current analysis.