After studies have been screened and prioritized, the next step is to assemble the final discovery outputs.
Included study assembly is the process of converting screened and prioritized records into a structured package that can be used for downstream data acquisition.
This step is important because the output of dataset discovery should not be a vague list of interesting studies.
It should be a documented, organized, and acquisition-ready input package.
Screened Studies
↓
Prioritization Table
↓
Included Study Assembly
↓
CDI-DAS Input Package
↓
Data AcquisitionIncluded study assembly creates the formal handoff between the CDI Systematic Dataset Discovery workflow and the CDI Data Acquisition System.
Study prioritization identifies which eligible studies should move forward first.
Included study assembly organizes those decisions into files that can be reused by downstream workflows.
For CDI workflows, the most important handoff elements are:
These outputs allow CDI-DAS to begin with clear, documented inputs.
The included study assembly step uses outputs from earlier chapters.
Expected inputs include:
outputs/screened-studies.tsv
outputs/included-studies.tsv
outputs/review-studies.tsv
outputs/prioritization-table.tsvThe screened studies table preserves all screening decisions.
The included studies table records records that passed screening.
The review studies table records studies that may need additional checking.
The prioritization table records which included records should be used first.
For this guide, the primary BioProject is:
PRJNA802976This BioProject is prioritized as the main healthy human gut microbiome case-study accession.
It is carried forward because it supports a practical CDI-DAS handoff and provides run-level accessions that can be used for acquisition validation.
The primary test subset is:
SRR17868090
SRR17868091
SRR17868092These runs provide a small, controlled subset for testing the downstream CDI-DAS acquisition workflow before scaling to the full BioProject.
Using a test subset helps confirm that metadata retrieval, manifest creation, download planning, and validation steps work as expected.
A secondary comparison BioProject may be retained:
PRJNA322554This record is not the primary handoff accession.
Instead, it can be used as a comparison example when demonstrating technical differences, metadata review, sequencing layout, or acquisition-readiness decisions.
The main output of included study assembly is the CDI-DAS input package.
This package should contain the accessions and supporting records needed to begin data acquisition.
Expected outputs include:
outputs/cdi-das-input-accessions.txt
outputs/cdi-das-test-accessions.txt
outputs/included-study-package.tsvThe accession list provides the study-level handoff.
The test accession file provides the run-level subset for validation.
The included study package provides the documented context for the handoff.
The included study package can be created with a script.
bash scripts/bash/08a-build-included-study-package.shThe expected outputs are:
outputs/cdi-das-input-accessions.txt
outputs/cdi-das-test-accessions.txt
outputs/included-study-package.tsvThese files prepare the discovery outputs for downstream use in CDI-DAS.
The included study package may contain:
Example:
package_id accession accession_type downstream_role
PKG001 PRJNA802976 BioProject Primary CDI-DAS input
PKG002 SRR17868090 SRA Run Test subset accession
PKG003 SRR17868091 SRA Run Test subset accession
PKG004 SRR17868092 SRA Run Test subset accessionThis structure makes the handoff explicit and reproducible.
The CDI Data Acquisition System begins from accessions.
For this guide, the systematic discovery workflow hands off:
Primary BioProject:
PRJNA802976
Primary test subset:
SRR17868090
SRR17868091
SRR17868092This allows CDI-DAS to retrieve metadata, build manifests, download files, validate data, and assemble a reference dataset package.
CDI Systematic Dataset Discovery
↓
Included Study Package
↓
CDI-DAS Input Accessions
↓
Metadata Acquisition
↓
Download Manifest
↓
Data Download
↓
Data Validation
↓
Reference Dataset PackageA clear handoff prevents confusion between discovery and acquisition.
Dataset discovery answers:
Which studies should be included, and why?
CDI-DAS answers:
How do we retrieve, validate, and organize the data reproducibly?
Keeping these systems separate but connected makes the overall workflow easier to explain, test, reuse, and scale.
Before handing off to CDI-DAS, confirm that the following are available:
Included BioProject selected
↓
Primary test subset defined
↓
Screening decision recorded
↓
Prioritization reason documented
↓
CDI-DAS input accession file created
↓
Test accession file created
↓
Included study package assembledThis checklist helps ensure that discovery outputs are ready for acquisition.
For the healthy human gut microbiome case study, the assembled handoff package should contain:
| Field | Value |
|---|---|
| Primary BioProject | PRJNA802976 |
| Primary test run 1 | SRR17868090 |
| Primary test run 2 | SRR17868091 |
| Primary test run 3 | SRR17868092 |
| Secondary comparison | PRJNA322554 |
| Downstream system | CDI Data Acquisition System |
| Handoff status | Ready for acquisition testing |
This confirms that the discovery workflow has produced a usable input package.
This chapter assembles the generic handoff outputs.
The next chapter applies the full workflow as a case study.
The case study will show how the healthy human gut microbiome example moves from research question to prioritized public BioProject and then into CDI-DAS-ready accessions.
Included study assembly converts screened and prioritized records into a structured CDI-DAS input package.
For this guide, PRJNA802976 is assembled as the primary BioProject accession, while SRR17868090, SRR17868091, and SRR17868092 are assembled as the primary test subset.
PRJNA322554 remains available as a secondary comparison record.
This chapter creates the bridge between systematic discovery and reproducible data acquisition.
In the next chapter, we apply the complete workflow to the healthy human gut microbiome case study and show how the selected public study becomes ready for CDI-DAS acquisition.