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