December 6, 2024
We are pleased to announce a new version of FAIRDOM-SEEK is now available, which is version 1.16.0
This is a large new version, and highlights include:
- FAIR Data Station Integration - new work carried out as part of BioIndustry4.0 and with contributions from
PhenomUK (for improved MIAPPE support).
FAIR Data Station provides a lightweight approach to gathering, validating, and ingesting metadata through the use of
spreadsheet templates and following FAIR principles.
Current support includes:
- The introduction of (optional) Observation Units, that fall between Study and Sample in the ISA structure.
- Ability to import the metadata produced by the FAIR Data Station, following validation of a spreadsheet template. And also afterwards should the template change, allowing updated, additions and items moving (but not deletion).
- Allows the registration and updates of the full Investigation, Study, Observation Units, Samples, Assays and registration of Data Files.
- Matches metadata attributes configured in FAIR Data Station with those of pre-configured Extended Metadata Types which are then automatically applied.
- This is currently an experimental feature, disabled by default (but can be enabled in the settings), with documentation planned, and also automatic creation of Extended Metadata Types, tighter coupling through API’s and RO-Crate support.
- Explicit Sample Type permissions - previously, Sample Type visibility was automatically derived according to the Projects it is shared with and the visibility of related Samples. This has now been updated to allow the permissions to be explicitly defined and under user control. When upgrading SEEK permissions will be set that mirror the old derived permissions.
- Fewer constraints on editing Sample Types - previously, once a Sample Type has Samples created from it, the ability to change the attributes was limited. This has been relaxed to allow some changes to be made that won’t invalidate existing Samples, including adding new optional attributes, changing attributes from required to options, the title attribute, the attribute pid and description, and changing the name of an attribute.
- Creating new Extended Metadata Types - an instance administrator of SEEK can now create new Extended Metadata Types through the user interface, using a simple JSON file that defines the type and attributes. The JSON has a corresponding schema against which it is validated. There is new extensive Documentation including on on how to create, and we are also planning on supporting doing so with an Excel template.
- Deleting Extended Metadata Types - in addition to being able to disable, an administrator is now able to delete Extended Metadata Types.
- RDF support extended to support Extended Metadata and Samples - RDF generation will now include Extended Metadata when present for the attributes that include an identifier, and similarly some basic RDF is generated for Samples.
- DataHub enhancements including
- Implementation of Assay Streams to group multiple assays that share similar traits like the technology type.
- Better integration of ISA-JSON compliant items.
- Improved sample querying using the Experiment Sample Template Attributes.
- Registering multiple Datafiles via a zip file - a contribution from PhenomUK, that allows multiple DataFiles to be registered at once by uploading a zip file.
- Search improvements - to better support non-ASCII characters, such as umlauts and accented characters. Now both the original and closest ASCII representation are indexed.
- COPASI model simulation - enables the interpretation and manipulation of COPASI models directly within the SEEK client interface, using COPASI.js.
- WorkflowHub enhancements including
- Improved support for importing workflows from Github, which is also now configurable and handles versions better.
- Improved support for RO-Crates, and submitting RO-Crates through the API.
… and much more.
More details about what changes are included can be found in the 1.16.0 Release Notes.
Details on installing SEEK can be found in our Documentation, at https://docs.seek4science.org/get-seek.html – including running with Docker.
The upgrade guide can be found in the usual place at https://docs.seek4science.org/tech/upgrading.html.
Details on upgrading for Docker can be found on the page https://docs.seek4science.org/tech/docker/docker-compose.html.