BentoPlatform

Changelog

Releases

Version history for the Bento platform, newest first.

  1. Version 26

    Current2026-09-01

    Major milestones

    • Better chart layout logic and a compact mode for chart dashboards (overviews).
    • Spreadsheet export column controls for authorized users.
    • XLSX data export for authorized users.
    • Better accessibility for visually-impaired users in the data catalogue.

    Other features

    • Small fixes for the data catalogue.
    • Fixes for choropleth maps.
    • Translatable month-year bins in search and charts.
    • A new "Admin" link in the footer in place of the previous header "Portal" link.
    • Customizable default charts per chart section for deployers.
    • Various PCGL-specific improvements.

  2. Version 25

    Released2026-08-05

    Major milestones

    • Data Catalogue Design
    • Enabled Summary Charts in the Data Catalogue
    • Redesign of the Provenance Display
    • Replace about text with dataset (long-)description in project/dataset view
    • French Translations for Datasets

    Other features

    • Users with smaller screens will be able to fit more charts on-screen at once with an improved chart layout and an optional compact mode.
    • Authorized users will be able to select columns of interest when exporting tabular data, and export Excel files directly from Bento.
    • For multi-dataset instances, the data catalogue will improve accessibility for visually impaired users.

  3. Version 24

    Released2026-06-30

    Major milestones

    • Move faceted search to the sidebar on project–dataset pages, displaying counts next to each filter for instant context while searching.
    • A new data catalogue header, modernizing the page header while preserving all existing functionality and backward compatibility.
    • Support creation of new datasets with the new dataset model, ensuring compliance with the new structural validation rules — including creation of fields and constraints, validation errors for missing or invalid fields, and reliable storage and retrieval of newly created datasets.
    • Support the new dataset model for Bento Public, with public access now available for the new dataset endpoint, including data display and translation loading.
    • Biosample pop-over feature, letting users preview key details about a biosample before opening it to quickly assess whether it has the information they need.

    Other features

    • Implementation of the Bento Data Catalogue Design.
    • The new Provenance display.

  4. Version 23

    Released2026-05-27

    Major milestones

    • Support multiple values ("OR" queries) for filters in the UI — select multiple options for a filter and see results matching any of them.
    • Add a user interface for custom range queries, letting authorized users search arbitrary ranges of dates or numbers in Bento Public rather than fixed bins.
    • New dataset model — a new dataset provenance model for metadata about datasets ingested into Bento instances.
    • Grant editing user interface, letting administrators manage access more easily without leaving Bento Web.

    Other features

    • Enhanced Data Catalogue header, giving a high-level overview of the instance and a customizable branding element for instances.
    • Interactive biosample popovers — hover over a biosample ID for immediate details, or click to open the full biosample on the relevant phenopacket page.
    • New dataset model support in Bento Public.

  5. Version 22

    Released2026-03-16

    Major milestones

    • Fuzzy search — rather than requiring an exact match, returns results that are close to the entered terms.
    • Biosamples linked experiment view, making it easier to navigate experiment-related information in the phenopacket view when sufficient permissions are available.
    • Pop-over tooltip for genome assemblies, showing key genome information and relevant links on hover over a reference genome ID.
    • Highlighting entities in the phenopackets view — clicking an individual, biosample, or experiment highlights it.
    • Highlighted dataset counts for search results, showing the number of matching entities in the dataset card for multi-dataset project searches.

    Other features

    • Organize and automate how external data is loaded into Bento data services.
    • Search arbitrary ranges of numeric fields, for users with sufficient privileges.
    • Portal administrators can post-hoc ingest files and associate them with existing experiment results.
    • Researchers can use a compact URL representing the hierarchy of their location on the site.

  6. Version 21

    Released2026-02-06

    Major milestones

    • The experiments table in the phenopacket detail view now shows "Biosample ID" with links to other data in the tabs above, and the corresponding column under "Sampled Tissue"; the biosamples row is expandable.
    • Phenopackets are downloadable directly from the Bento Public research portal.
    • A button (×) in the text search box to clear the search text.
    • Counts (vertical axis numbers) are displayed above the bar charts.
    • Navigation now lets users move forward to a new page without losing their position on the original page — going back, or refreshing, restores where they left off.
    • A back button to return to the search from the detail view.

    Other features

    • Ontology class-aware discovery functionality, including looking up records by ontology term values.
    • Users can see all datasets at once in the public Data Catalogue.
    • Users can view the dataset using a dataset model in the Provenance tab.
    • Stricter authorization — users without permission can no longer see or use the "Explore" button.

  7. Version 20

    Released2025-11-28

    Major milestones

    • Biosamples can display collection locations as a map or as coordinates, mostly intended for non-human datasets.
    • Experiments and experiment results are visible in Bento Public.
    • A compact view for phenopackets, showing everything on one page rather than navigating through tabs.

    Other features

    • Improved text search for better full-text search results.
    • Entity counts for projects and datasets are displayed in the data catalogue.
    • Units are viewable in the field description of the interface.
    • Users with sufficient permissions can export all search results as CSV, not just the current page.

  8. Version 19

    Released2025-10-31

    Major milestones

    • Merging bento-web and bento-public: fine-grained data exploration available from the same interface as the aggregate data view, based on user authorization level.
    • Object store support for all data services, with the S3 API.

  9. Version 18

    Released2025-02-05

    Major milestones

    • Datasets catalogue — a way to explore projects and datasets stored on a Bento node.
    • Releasing Takuan, a new service to index and search transcriptomics data.

    Other features

    • Authorization service added to the Katsu metadata service.
    • Now possible to ingest any file type as experiment results into DRS.
    • Optional MinIO deployment now available.
    • Improved branding features for Bento instances, e.g. customizable dark and light background logos.

  10. Version 17

    Released2024-10-04

    Major milestones

    • Scope: multiple projects and datasets/cohorts are now supported in aggregate data exploration tools.
    • Beacon Network: query multiple Bento nodes using the Beacon v2 API, and present results together.
    • Enabled logs monitoring in all Bento services using Grafana.

    Other features

    • Authenticated users get more fine-grained responses in the aggregate data exploration tools.
    • Variant search on non-human genomic data (requires a reference ingested in the reference service).
    • DATS provenance metadata can now be ingested/downloaded as a JSON document.
    • Beacon variant search by gene ID.

  11. Version 16

    Released2024-07-23

    Major milestones

    • Support for cBioPortal as a service within Bento, including a VCF-to-MAF conversion workflow and a minimal set of clinical/biosamples data available through cBioPortal.
    • Authorisation service: create grants and manage users and groups from the user interface.

    Other features

    • New Bento interface to explore aggregate data.
    • Support for data files on object storage.
    • Reference service now ingests GFF3 annotations.

  12. Version 15

    Released2024-01-10

    Major milestones

    • Migration of clinical and phenotypical data model to Phenopackets v2.
    • New reference genomes service, allowing ingestion of the assembly used with a dataset (e.g. for non-human datasets).
    • Authorisation service, limiting access to administration and data ingest tools, with uncensored counts for authenticated users.

    Other features

    • User interface improvements for Bento Public (aggregate information).
    • Authentication into Bento Public to run full Beacon searches.

  13. Version 14

    Released2023-11-02

    Major milestones

    • Documents other than genomic files and annotations can now be ingested as experiment results.

    Other features

    • Beacon record-level queries for authorised users.
    • Experiment results and drop box files can now be visualised from the interface (PDF, CSV, audio/video files, etc.).
    • UI improvements in the public Overview and Provenance tabs.

  14. Version 13

    Released2023-09-08

    Major milestones

    • Removal of the Tables concept — data is now organized by Project > Dataset > Data Type.

    Other features

    • API endpoint to extract provenance metadata (DATS format).
    • Show latest ingestion date on the public site.
    • Ingestion errors available in workflow execution runs.