Last modified 2026-01-27

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Ingest an Olink Manifest (Tutorial)

Abbreviations Key
CSVcomma-separated valuesPDFportable document format
HISEHuman Immune System ExplorerSDKsoftware development kit
IDEintegrated development environmenttartape archive
KTkit.xlsx.xml-based Excel file format
NPXnormalized protein expression

At a Glance

This document explains how to use a submission sheet to ingest an Olink manifest and its associated data file into HISE. The Olink manifest documents the plate layout and sample IDs that the submitting lab prepares to accompany the physical samples sent to the Olink provider. The Olink data file contains the assay results for these samples (for example, NPX values and related measurements). The Olink submission sheet is an AIFI-specific file that configures the data ingest pipeline and links ingested files to studies, assays, and sample IDs.

When all prerequisites are met and the manifest and data file are ingested, HISE automatically tags the Olink manifest with the sample IDs it contains. This enables downstream use in HISE IDEs by adding sample metadata to the file descriptor when files are read from the SDK. If you have questions or need help, contact Support.

Ingest Process

Role of the Olink manifest decorator

Olink data is ingested by dropping files into a watchfolder. The files are processed by an Olink manifest decorator. If processing succeeds, the Olink data file is tagged with sample references, and the Certificate of Analysis (PDF) is tagged with the sample IDs declared in the manifest but not listed in the data file.

Constraints for multi‑account files

When a single Olink data file contains samples from multiple accounts, the following constraints apply:

The following code helps you split Olink data files into separate, account‑specific files. You can use the code as is or adapt it for your own tooling. To use it, however, you must have Go (golang) installed.

./olink-ingest help
./olink-ingest help splitparquet

Instructions

 Sign in

1. Navigate to HISE, and use your organizational email address to sign in.

 Acquire data and sample manifest files

1. When Olink Services notifies you that your data is ready, access the zip file at us.mydata.olink.com . If you don't have access, ask someone on your team to help you, or file a Support ticket.

2. Unzip the Olink Google Drive folder, and confirm that it contains the files listed in Table 1.

TABLE 1

Olink folder contents

TypeFormatPurpose
Certificate of AnalysisPDF
  • Specifies the account or project into which the data should be ingested
  • Specifies whether the data must be split across accounts
Data file.xlsx, .csv, or .parquet
  • Needed to create the HISE submission sheet

 Create a HISE submission sheet

To create a HISE submission sheet via a watchfolder ingest, you must first create a manifest file that lists all specimen IDs found in the Olink data file.

1. Set up a manifest file as shown in Table 2.

A. Place the unique sample ID (the anonymized ID sent to Olink) in column index 2.

B. Place the AIFI specimen ID (the ID used by HISE) in column index 4.

TABLE 2

Example manifest

ABCDE
1Plate IDWell IDUnique sample IDSample IDAIFI Specimen ID
2

1

A2

652527655222

KT11267

SR11267-001

31A3

680243353312

KT11248

SR11248-001

41A4

622312080728

KT11035

SR11035-001

2. Save the manifest file in .csv or .xlsx format, using the naming convention shown in the accompanying box.

Naming convention for manifest files

Olink_Manifest_<SubmissionID>.csv

(or .xlsx)

Example file name
Olink_Manifest_q-04064.csv

3. Drop the manifest file into the appropriate watchfolder for processing by the Olink manifest decorator, which creates a HISE submission sheet. This document is used later to tag the data file with the corresponding sample IDs.

4. Validate the HISE submission sheet here. If the specimen IDs declared in the manifest do not yet appear in HISE, the sheet will fail validation. If this occurs, contact Support.

Sometimes samples from multiple initiatives are submitted to Olink together. When this happens, each account must have its own HISE submission sheet containing only the samples associated with it.

  Separate the data for multiple accounts

This step is required only when a single Olink batch contains data for multiple accounts.

1. To create separate data files from the original Olink file, run one of the commands shown in the accompanying box.

Separating data for multiple accounts

Parquet files

./hisecli splitparquet <data_file> <manifest_file> <file_postfix>

file_postfix is appended to the output file name.

Examples
Input file
Output file
EDTA_plasma.parquetEDTA_plasma_<file_postfix>_split.parquet
Excel files

./hisecli splitxlsx <data_file> <manifest_file>

  Tar and ingest the data 

If the data was split for multiple accounts, you must repeat this step for each account.

1. Create a tar archive containing the following files. Use the naming convention outlined in the accompanying box.

A. Olink data file

B. Certificate of Analysis (PDF)

Naming convention for tar files

Olink_<SubmissionID>.tar
Example file name
Olink_q-04064.tar
Example terminal command
tar cvf Olink_<SubmissionID>.tar <path_to_files>

2. Drop the tar file into the watchfolder for the appropriate account. For complete instructions on creating a tar file, see Submit and Monitor Pipeline Batches (Tutorial). If you need help, contact Support.

Related Resources

Configure a Pipeline (Tutorial)

Use Watchfolders to Ingest Data (Tutorial)

Understand Automated Pipelines (Tutorial)