This is a patch release that includes some bug fixes and improvements, including:

• Inline document preview, previously only available on Presentation pages, is now also available for SOPs, Documents, Data files and File templates.
• Institution pages now show a link to the full ROR profile, rather than just the ROR ID.
• SEEK now fails fast with a clear error if the database is unreachable at startup, rather than silently falling back to defaults and causing confusing behaviour.
• Improved database performance for Samples, through additional indexes.
• CSV files with non-UTF-8 encodings are now handled gracefully, rather than causing an error.
• DataHub improvements including:
  • Units can now be set, and locked, on attributes in global ISA sample type templates.
  • Fixes to registered Data files, Strains and SOPs not appearing correctly in the experiment view.
  • Fixes to applying Extended Study Templates when creating an Assay.
• WorkflowHub improvements including:
  • Updated support for the RO-Crate 1.3 specification.
  • Better validation and error handling when adding files to Git-backed workflow versions.
  • A fix to an error that prevented new workflow versions being submitted.
  • CITATION.cff files are now validated before being converted to BibTeX.
• Various library and security updates.

There are several more changes, details of which can be found in the 1.18.1 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

Day 5 teaches Research Data Management, featuring FAIRDOM SEEK from eductors Ulrike Wittig and Wolfgang Müller (HITS, de.NBI SysBio).

For details, please visit the event page on the de.NBI website.

This is a large new version, and highlights include:

• DOI enhancements:
  • Presentations can now have DOIs minted and retracted, alongside other asset types.
  • Resources with DOIs can now be deleted, with automatic DOI retraction and metadata storage.
  • Publication types are automatically detected when querying DOIs during registration.
• New administrator options:
  • Prevent local file uploads, requiring remote URLs instead.
  • Disable built-in username/password login to enforce SSO-only access.
• Search improvements:
  • Samples are now fully supported in API-based searches and returned in search results.
  • External search adapters can be toggled via the admin settings UI.
  • Search now handles punctuation correctly (hyphens, parentheses, etc.).
• Extended Metadata improvements:
  • Controlled vocabulary attributes can now accept free text when configured.
  • Nested Extended Metadata attributes export as blank nodes in RDF.
  • Fair Data Station imports correctly reject type mismatches with required fields.
• Events now support event types with hybrid, online, and offline location options, and end date auto-sets to 1 hour after start date selection.
• ISA & DataHub enhancements:
  • Temporary sharing links for ISA assets (Investigations, Studies, Assays, Observation Units), providing time-limited access via authorization codes.
  • ISA input tag now available through the API.
  • Global sample type templates can now reference registered assets.
  • Extended metadata fields are now included in spreadsheet exports.
• Workflow enhancements:
  • New workflow versions can be created via RO-Crate upload.
  • Bioschemas/schema.org properties expanded for workflows, including creativeWorkStatus, contributor, citation, and datePublished.
• Multiple security vulnerabilities (XSS) addressed.
• PDF preview rendering greatly improved.

… and much more.

More details about what changes are included can be found in the 1.18.0 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.

Please note that this upgrade requires some additional attention in two areas:

• Solr configuration — to pick up the search improvements, the Solr configuration needs to be updated. Details can be found at https://docs.seek4science.org/tech/setting-up-solr#updating-the-solr-configuration.
• Docker Compose — the compose files follow a new structure, and the Solr service has been updated to use the official Solr image directly, with configuration files now needing to be provided under solr/seek/conf. Full details are at https://docs.seek4science.org/tech/docker/docker-compose#updating-the-solr-configuration.

This is a patch release that includes some important bug fixes and improvements, in particular:

• Fix to BioModels external search throwing a 404 error in some cases.
• Fix to search indexing of markdown content, to correctly strip out HTML tags.
• Fix to permissions to download Sample type templates, they are now always available if the Sample type is visible.
• Institution departments are now shown when adding a new member to a Project.
• Fix to apply selected attributions when creating a new Data file.
• Fix to SPDX license information not being correctly imported from Workflow RO-Crates.
• Fix to an unexpected nil error during batch delete when using DataHub’s dynamic table.
• Fix to include the latest instance name when downloading a spreadsheet from DataHub’s single page view.

More details about the changes can be found in the 1.17.4 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

In March 2026, we hosted the first FAIRDOM Collaboration Fest (CoFest) online. Users, developers, leaders and advocates from nine institutions in six countries created an opportunity to collaborate, discuss and progress a range of matters and features which will be of benefit to the wider FAIRDOM-SEEK community. We also welcomed those interested in learning more about FAIRDOM-SEEK and how it could benefit their work.

The mini CoFest format allowed us to discuss and plan upcoming work, without needing to commit any code immediately. We presented two topics, covering a range of concepts and teams.

Recap of FAIRDOM-SEEK features released in 2025

The session opened with a brief review of the FAIRDOM-SEEK features released since the Mini Hackathon event we ran in February 2025. These include improved support for FAIR Data Station, enhanced Schema.org metadata support, a new SPARQL view, support for DataCite-based DOIs for publications, and improvements to WorkflowHub and NeLS. Such features were possible thanks in part to your contributions at the Mini Hackathon.

Topic 1: Knowledge Graph and Linked Data

Knowledge graphs are an increasingly useful method for representing research data. FAIRDOM-SEEK can easily be configured to publish a queriable public knowledge graph of all open content, and optionally a private graph of all content. This project, led by Stuart Owen (University of Manchester) with Xiaoming Hu (Heidelberg Institute for Theoretical Studies) and Phil Reed (University of Manchester), provided a comprehensive overview:

• Introduction to Linked Data and RDF, and their benefits
• How FAIRDOM-SEEK supports Linked Data by describing objects using JERM-based RDF, Schema.org and Bioschemas markup, and JSON-LD
• How FAIRDOM-SEEK includes Extended Metadata and Sample properties within the RDF
• How FAIRDOM-SEEK uses the Sample bioschemas type, and includes custom properties using PropertyValue
• The new SPARQL view in FAIRDOM-SEEK, providing access to the public knowledge graph, with customizable example queries
• A brief overview of the interoperability and integration between FAIRDOM-SEEK and FAIR Data Station
• A demonstration of how to set up the knowledge graph on your SEEK instance using Virtuoso
• A look at how RDF is generated from a customizable lookup table

The presentation concluded with a look at the future plans for developing knowledge graphs in FAIRDOM-SEEK. Suggested work includes the addition of Schema.org in the knowledge graph, enriching the RDF with external identifier info (ROR and ORCID), and discussing how RO-Crate might be included in the graph. Also under consideration is to include Extended Metadata in the Schema.org markup. These plans are subject to change; please follow the Roadmap to keep updated.

Topic 2: Neo4J, Visualization and LLM enabling

The FAIRDOM-SEEK platform enables the building of project hubs where investigators can store, share, access, connect and interact with digital objects generated from their research, and use them in their own analyses. MIT BioMicroCentre uses a private hub called NExtSEEK within the MIT facility to coordinate project management during the running of a project. The second topic at the FAIRDOM CoFest was led by Charlie Demurjian (MIT), and described how NextSEEK is developing an agentic team to interpret natural language to query its database. Highlights of the presentation:

• NextSEEK provides active data management as a wrapper around FAIRDOM-SEEK.
• Samples in NextSEEK can be visualized in a tree, powered by Noe4J.
• To make something “LLM Ready”: separate the work into small agentic tasks, give specific instructions in a workflow, where each agent has concrete input and output schemas and contexts.
• Develop the processes using published data, in this case, 50,000 samples.
• Start on use cases that are things you can already do on the website, establish a base truth, keep the human in the loop.
• Work up to queries such as “Build me a GEO Submission for D.SEQ-221031SHA-67-PUB and D.SEQ-221031SHA-65-PUB”. NextSEEK Assist can build a GEO spreadsheet for two given samples. The agents will go up and down the tree to map to the correct fields in the GEO, generate an Excel workbook with strategy, treatment and protocols for the researcher as their starting step. This will make researchers’ lives easier.

The presentation concluded with a look at the roadmap for LLM-supported work in NextSEEK. One path is network ingestion (to populate the SEEK database), another is to interoperate with sequencing pipelines (from a repository submission, given sequencing files, run a Nextflow pipeline and bring the results back into SEEK). Many of the approaches and lessons learned could be shared across the FAIRDOM consortium and may apply to other instances of FAIRDOM-SEEK.

Following up

Slides

• Main Presentation, Topic 1, Topic 2 (FAIRDOMHub)

Video

• Main Presentation, Topic 1 (YouTube)

If anyone is interested in collaborating with any of the presenters above, please get in touch directly (or contact us). Our next FAIRDOM user meeting will run in early autumn 2026, check back here for details.

This is a patch release that includes some important bug fixes and improvements, in particular:

• Fix error handling and reporting when trying to export PubMed based publications without the email used to access the PubMed API being configured.
• Bugfix for exporting samples from ISA-JSON compliant assays and studies to an Excel spreadsheet in the default view.
• Fix to an error when uploading content to an empty content blob when using the API.

More details about the changes can be found in the 1.17.3 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

We invite you to register for the FAIRDOM Collaboration Fest (CoFest) Online. Users, developers, leaders and advocates will have an opportunity to collaborate, discuss and progress a range of matters and features which will be of benefit to the wider FAIRDOM-SEEK community. We also welcome anybody interested in learning more about FAIRDOM-SEEK and how it could benefit their work.

The event will run on Zoom on Monday, 2 March 2026 for 2 hours, providing opportunities for people in eastern North America, western/central Europe and western/central Africa to work together.

• Learn about FAIRDOM-SEEK features released in the last 12 months, thanks in part to your contributions at the FAIRDOM Mini Hackathon in February 2025.
• Topic 1: Knowledge Graph and Linked Data. Join a discussion about querying the public knowledge graph of a FAIRDOM-SEEEK instance, through writing SPARQL queries, using Triple Stores and Extended Metadata.
• Topic 2: Visualization and LLM Enabling. Watch a presentation about how Neo4J, visualization tools, and Large Language Models (LLM) have been combined in NextSEEK to vastly reduce the time bioinformaticians spend filling out GEO forms.

For full details and to register, please visit the FAIRDOM CoFest Online 2026 event page.

This is a patch release that includes some important bug fixes and improvements, in particular:

• A new SPARQL view, that allows SPARQL queries to be made over the public graph directly in SEEK, if running together with the Virtuoso triple store.
  • Ability to execute queries and store the URL of queries for later re-use.
  • Configurable set of predefined example queries.
• Added support for registering DataCite based DOIs, in addition to CrossRef based DOIs. Alongside this the list of Publication types have been expanded to include those supported by DataCite.
• Fixes related to registering Publications as Bibtex files.
• Fix to the rendering of Publication abstracts.
• Expanded the list of Model types, execution environments and formats to support Machine Learning models.
• Enhanced the schema.org metadata support
  • to include identifiers for DOI, ROR and ORCID
  • added LabProtocol (from Bioschemas) as a type for SOPs.
  • fixed the JSONLD endpoint to be available for all items that support schema.org metadata.
• Reduced the batchsize when reindexing all items from 250 to 50, and made configurable through Seek::Config.reindex_all_batch_size.
• Fix to better handle requesting invalid citation styles. Previously an invalid style would become the default style, leading to subsequent errors.
• DataHub specific:
  • Return to the single page view when cancelling from an items Manage page.
  • Fix propagating permissions to child Assays and Sample types.

More details about the changes can be found in the 1.17.2 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

This is a patch release that includes some important bug fixes and improvements, in particular:

• A minor update to Rails (7.2.2.2) and various libraries for bug and security fixes.
• An update to use version 2 of the ROR API.
• Projects can now specify scientific disciplines, which can then be used for filtering. The disciplines are defined by the OpenAlex classification.
• There is now a check that creators exist before creating a DOI, notifying the user if missing to avoid an error.
• A fix to prevent errors occurring following the deletion of a Collection avatar.
• UI improvement to allow multiple lines of copyright text to be configured.
• UI improvements to the registration page, when there are third-party authentication options configured (e.g. LS Login).
• Licenses are now displayed to also include the short form, which is sometimes more familiar to users.
• Fix to correctly display the preview of the name of a Creator when typing.
• Fix to an incorrect date being displayed when close to a timezone difference.
• Improvements and fixes to manually providing Publication authors, including now searching for registered users and better support for pasting a comma separated list.
• WorkflowHub improvements including:
  • Scientific disciplines are propagated from Projects (Teams) to Workflows automatically.
  • Workflow RO-Crate fixes to include datePublished, and removed WorkflowSketch as the type.
• DataHub improvements including:
  • Dynamic Table improvements.
  • JSON-ISA export fixes.
  • Units should be transferred from Templates to Sample Types.
  • Added ISA compliance as a filtering option.
  • Assay stream fixes.
  • Fix for downloading samples as Excel.

More details about the changes can be found in the 1.17.1 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

Taisha Joseph (MIT, USA)

• “Next in NExtSEEK: AI Meets Labeled Property Graphs for Smarter Data Management”

Jasper Koehorst and Brett Metcalfe (Wageningen University & Research, Netherlands)

• “Integration of FAIR Data Station with FAIRDOM-SEEK”

Thiranja Prasad Babarenda Gamage (Auckland Bioengineering Institute, New Zealand)

• “SEEK Meets DigitalTWINS: Enabling Development and Clinical Translation of Virtual Human Twins”

The FAIRDOMHub is built upon the FAIRDOM-SEEK software suite, which is an open source web platform for sharing scientific research assets, processes and outcomes. For more information about FAIRDOM-SEEK please visit our FAIRDOMHub page.