Ontologies are powerful tools to integrate data from different sources (interoperability of data). There are several terminology services worldwide, including NCBO BioPortal, the ELIXIR service EMBL-EBI Ontology lookup service (OLS) and the OLS-derived TIB terminology service.

In ELIXIR, ontologies are used in metadata annotation with Bioschemas, ELIXIR deposition database MetaboLights or EDAM in bio.tools and TeSS. Several NFDI consortia in the life-sciences also integrate ontologies in their services. To simplify the integration, packages and libraries for different programming languages can be used. 

A challenge is the sheer number of ontology terms matching a simple substring search on an entire terminology service. Hence, applications should recommend specific ontologies for specific term annotations, or even a specific ontology branch to be searched. Machine learning methods support the Named Entity Recognition further. 

Several hacking topics have been identified by prospective participants already:

  • Terminology Service Department: Managing and serving terminologies
    • Best practices for creating and validating richly described FAIR ontologies
    • Integration of a validation pipeline into terminology services
    • Developing components for terminology services
  • Consumer Department: Connecting clients to the terminology services
    • HTML widgets to display / pop-up term details for re-use by ressources
    • Clients / HTML widgets to support term selection
    • Integrating the TS into ressources like ELNs and data repositories
  • Search and Validation Department: making sure the right terms are used in the right place
  • Training and outreach Department: 
    • training material / overview of other (existing) tooling around terminology services
    • tell people about the Hackathon project and its results

Project Lead: Steffen Neumann <This email address is being protected from spambots. You need JavaScript enabled to view it. and Oliver Koepler <This email address is being protected from spambots. You need JavaScript enabled to view it.>