diff --git a/docs/user-guide/supported-data/supported-data.md b/docs/user-guide/supported-data/supported-data.md index 7f1cb547..caa79156 100644 --- a/docs/user-guide/supported-data/supported-data.md +++ b/docs/user-guide/supported-data/supported-data.md @@ -163,6 +163,44 @@ in our **Advanced User Guide**. ## HDF5 (e.g. Single Cell) +!!! info "Limitations" + HDF5 is supported as Attached File in ODM with ability to observe and search by File Structure (Contents) only. + We are working on full functionality for HDF5 data content parsing, search, and filtering. + +**HDF5 (Hierarchical Data Format version 5)** is a widely used data format in genomic research, particularly in +Single Cell studies. It is designed to store large, complex datasets efficiently, making it a preferred choice for +structured biological data such as gene expression matrices and metadata. + +The ODM now supports HDF5 file upload as Attached File, search by File Structure (Contents), and manage these +files within Studies. + +### Supported HDF5 Formats + +- **.h5, .h5ad** - Standard HDF5 files +- **.h5.gz, .h5ad.zip** - Compressed versions of standard HDF5 files + +### Viewing File Structure (Contents) + +- **Access File Contents via GUI**: The ODM displays File Contents on the Data Tab of Metadata Editor. It is + accessible on `Contents` button click. +- **Retrieve File Contents via API**: You can retrieve File Contents for the list of files or by unique + Genestack Accession. + +### Searching HDF5 Files by File Contents + +Users can search via GUI and API for: + +- **Unique File**: by Genestack Accession. +- **Files**: + + - By File Contents fields/pathways. + - By Study Genestack Accession. + +- **Studies**: + + - By File Contents fields/pathways. + - By File Genestack Accession. + For a detailed description and instructions on using HDF5, visit the **[Supported Data Formats page](../doc-odm-user-guide/supported-formats.md)** in our **Advanced User Guide**.