Table 1:
Use cases involving Bgee as a data producer along with the implemented interoperability approaches.
| Target knowledge base (KB) | Interoperability approach | Description |
|---|---|---|
| NCBI Gene [33] | One-side | Bgee must comply with the NCBI LinkOut system exchange file format, which is either a CSV or XML file. |
| UniProtKB [15] | One-side | Bgee must comply with the UniProtKB exchange file format, which is a text file based on its own format. |
| GeneCards [14] | Two-side | Bgee and GeneCards defined from scratch a TSV-like exchange file format that is easy and quickly consumed by GeneCards and produced by Bgee. |
| OncoMX [34] | Two-side | At first, Bgee and OncoMX defined from scratch a TSV-like exchange file format that was easy and quickly consumed by OncoMX and produced by Bgee. |
| RIKEN Metadatabase [35] | One-side | RIKEN Metadatabase directly imports the downloadable Bgee RDF dump file into its triple store as a named graph. |
| Monarch Initiative [36] | One-side | The Monarch Initiative project uses the available Bgee download files as they are. |
| SPOKE [37] | One-side | The Bgee download files are used as they are to build a precision medicine knowledge graph. |
| Open Systems Pharmacology [38] | One-side | The Bgee download files are used as they are to build a KB of gene expression information for drug development. |
| Wikidata [25] | One-side | Bgee developed a bot using Wikidata Python APIs in order to automatically extract, transform, and load its data into Wikidata [39]. |
| Wikipedia [40] | One-side | Bgee implemented and integrated a software component in the existing gene infobox module [41]. This allows Wikipedia to dynamically retrieve Bgee data in Wikidata. |
| Google Dataset Search [42] | Multi-side | Bgee provides Schema.org-based metadata embedded in its webpages. These metadata are automatically retrieved and consumed by other systems that support Schema.org such as Google Dataset Search tool. |
| OncoMX federation | One-side | OncoMX directly uses the available Bgee MySQL database, called EasyBgee (i.e., a one-side interoperability), to federate both KBs. To do so, the federated data schema is composed of the OncoMX native relational data schema and a view for the EasyBgee data schema is defined along with mappings. |