Last modified 2026-01-27 |
Ingest an Olink Manifest (Tutorial)
| Abbreviations Key | ||||
CSV | comma-separated values | portable document format | |||
Human Immune System Explorer | SDK | software development kit | |||
IDE | integrated development environment | tape archive | |||
KT | kit |
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NPX | normalized 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.
When to Use This Feature
Use this feature when you want HISE to automatically recognize and tag Olink assay results with the correct sample metadata, using an Olink manifest and data file:
You’ve received Olink assay results (for example, NPX data) plus a manifest or plate layout and want them ingested into HISE without manual relabeling of samples.
You need HISE to link Olink data files and Certificates of Analysis to the correct studies, assays, and specimen IDs so that downstream IDE and SDK workflows use the right sample metadata.
Your Olink batch includes samples from one or more AIFI accounts and you want to avoid ingest failures, missing specimen links, or misrouted data caused by incorrect manifests or file organization.
Use this document to ensure that your Olink manifest setup and ingest workflow are correct before you drop files into a watchfolder. This tutorial is intended to complement the pipeline documentation listed in the Related Resources section at the bottom of the page.
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:
A separate manifest file is required for each account.
The data file must be split into account‑specific files.
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.
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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 | ||
Type | Format | Purpose |
Certificate of Analysis |
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Data file |
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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 | |||||
A | B | C | D | E | |
1 | Plate ID | Well ID | Unique sample ID | Sample ID | AIFI Specimen ID |
2 | 1 | A2 | 652527655222 | KT11267 | SR11267-001 |
3 | 1 | A3 | 680243353312 | KT11248 | SR11248-001 |
4 | 1 | A4 | 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(or Example file name |
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 accountsParquet files
Excel files
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Tar & 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
Example file name
Example terminal command
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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)