Status: PRODUCTIVE
Overview
BiodivPortal is a dedicated instance of the OntoPortal technology for biodiversity related terminologies. OntoPortal is a generic technology to build terminology repositories and catalogues. The OntoPortal system architecture is structured in several layers:
- The storage layer contains a triple-store which saves each terminology in a distinct graph, as well as other data (metadata records, mappings, users, etc.). This layer also uses: (i) Redis-based key-value storage for application caches and the Annotator dictionary datastore; (ii) Solr search engine to index terminology content for retrieval with the Search service.
- The model layer implements all the mechanisms to parse the terminology source files using the OWL-API and retrieve them from the triple-store using a built-in Object-Relational-Mapping library (GOO).
- The service layer implements the core OntoPortal services: Search, Annotator and Recommender.
- The API layer implements a unified API for all the models (e.g., Class, Instance, Ontology, Submission, Mapping, Review, Note, User) and services supported by OntoPortal. The API can return as default a JSON-LD format.
- The user interface offers a set of various views to display and use the services and components built in the API layer. The UI is customized for logged-in users and for groups/organizations that display their own subset of resources. Administrators of the OntoPortal instance have access to an additional administration console to monitor, and manage the content of the portal.
RDC Integration
BiodivPortal is part of the RDC mediation layer. It stores and manages a set of terminologies, standard schemas useful for mapping data and metadata into standard formats for processing and storage in the RDC semantic layer. BiodivPortal offers among others, services to (i) annotate concepts (ii) establish links between semantically related concepts (iii) make concepts referenceable via stable URIs and (iv) make concept versioning transparent.
Semantic search capabilities will be enabled through the Semantic Lookup Index, which stores information about concept synonyms, acronyms, common names as well as broader terms.
Getting started
BiodivPortal is available on biodivportal.gfbio.dev. Users can register to get an account and an API key.
User Guide
A comprehensive user documentation can be found on the BioPortal wiki page: https://www.bioontology.org/wiki/BioPortal_Help
Developer Guide
The API documentation can be found here: https://data.biodivportal.gfbio.dev/documentation
References
Links:
- Main instance: https://biodivportal.gfbio.dev/
- Code: https://github.com/BiodivPortal