OntoPortal BioMixer Visualizer

A standalone ontology visualizer for OntoPortal. This project replaces the legacy BioMixer embed while keeping its commonly used query parameters and fullscreen message contract.

The application is plain HTML, CSS, and JavaScript. It can be served directly by a Web server or embedded in OntoPortal Web UI.

Run locally

python3 -m http.server 8080

Open http://localhost:8080/.

A container image can be built and served on port 8000:

docker build -t biomixer-visualizer .
docker run --rm -p 8000:8000 biomixer-visualizer

The container serves both / and /visualizer/, matching the default OntoPortal deployment ingress path.

Embed parameters

The visualizer accepts these BioMixer-compatible parameters:

• mode=embed
• embed_mode=paths_to_root|term_neighborhood|mappings_neighborhood|ontology_mapping_overview|uml|diagram|print
• ontology_acronym, ontology, or acronym
• full_concept_id, conceptid, or class_id
• userapikey or apikey
• restURLPrefix

Optional integrations:

• sparql_endpoint, sparqlEndpoint, or sparql
• lodview_url, lodview, or resource_view_url; use {iri} as the encoded resource placeholder

Example:

http://localhost:8080/?mode=embed&embed_mode=paths_to_root&ontology_acronym=STY&full_concept_id=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT071&restURLPrefix=https%3A%2F%2Fdata.bioontology.org

OntoPortal integration

OntoPortal Web UI can serve these files itself or point to a separately hosted copy with ONTOPANEL_VISUALIZER_URL. The biomixer_replacement Flipper feature selects the replacement; the legacy BioMixer embed remains the default until that feature is enabled.

The public widget reads biomixer_replacement_enabled and ontopanel_visualizer_url from the existing site configuration endpoint.

Features

• paths-to-root, neighborhood, mappings, ontology atlas, and diagram views
• pan, zoom, node dragging, minimap, search, and keyboard controls
• class details, relations, selection history, and optional SPARQL queries
• SVG, PNG, JSON, diagrams.net, and PlantUML downloads
• print view and light/dark themes
• visible-node limits and paged atlas loading for large ontologies

Validate

node --check app.js

Open an embed URL and verify that ontology data loads from the configured OntoPortal API.

License

Apache License 2.0. See LICENSE.