This repository stores metadata templates in use at SciLifeLab, organized according to data type. The information flow between this repository, the data producing platforms and the data submitter with the end goal of data submission to a public end repository is sketched in the diagram below.
| Title | Description | Link |
|---|---|---|
| SciLifeLab Genomics Technical Metadata Template | This template aims to capture technical metadata for genomics data produced at the Genomics platform, compatible with submission requirements from ENA and ArrayExpress. | genomics/README.md |
A template has a title, a description and a semantic version number, as well as well as a list of associated attribute fields.
Within a template each technical attribute field needs to have:
- Field name: identifier for the attribute
- Level of requirement/cardinality (mandatory vs optional)
mandatory_for_data_producer: to be filled in by the data producing facility as far as possiblemandatory_for_data_submitter: to be filled in by the data submitter, not expected to be known by the data producing facility
- Description
- List of controlled vocabulary terms, if applicable
- Target (end) repository: end repository which this metadata attribute targets
- Target (end repository) field name: the exact name of the corresponding metadata attribute field at the end repository
In addition to data type specific fields capturing the technical metadata itself, all templates include additional organizational metadata such as
- SciLifeLab infrastructure platform and unit
- Unit internal project ID(s)
- Associated order ID
- Experimental Sample IDs (as assigned by the unit, 1 exp sample = 1 data file (pair))
- Associated Sample IDs (as shared by the researcher with the unit)
- Metadata file creation date
- Template name
- Template version
Templates are provided as .tsv, .json and .json schema. A row entry for an individual sample in a filled out .tsv would then correspond to the following information
| <data_type_specific_field1> | ... | <data_type_specific_fieldM> | <data_file_name_R1> | ... | <data_file_name_RP> | <orga_meta_field1> | ... | <orga_meta_fieldN> |
|---|
For questions relating to this repository and the use of its metadata templates at SciLifeLab in general, please contact [email protected] and put "metadata-templates" as a keyword. For specific questions about filled-in metadata files received together with data produced at SciLifeLab please contact the data producing unit directly.
This repository is maintained by SciLifeLab Data Centre and NBIS. The data-type specific metadata templates are created in collaboration with SciLifeLab data producing platforms. For contributors to individual metadata templates please see the relevant subsection on the specific template readme pages.