PPSDB : A Linked Open Data knowledge base for protist-prokaryote symbiotic interactions

As the ecological and evolutionary importance of symbiotic interactions between protists (microbial eukaryotes) and prokaryotes (bacteria and archaea) is better appreciated, keeping an overview of their diversity and the literature becomes a growing and ongoing challenge. Here we present the Protist-Prokaryote Symbiosis Database (PPSDB), comprising 789 manually curated interaction statements sourced from 410 publications, where biological taxonomy, anatomical localization, and analytical methods applied have been annotated and mapped to external databases and ontologies, such as Wikidata, NCBI Taxonomy and Gene Ontology. We describe how our data model deals practically with challenges such as incomplete information and inconsistent taxon concepts, which will be applicable to similar projects. Both the model and underlying Wikibase software platform are highly extensible, so new items and properties can easily be added. Unlike a static table or list of citations, PPSDB is a structured knowledge base that enables programmatic access and powerful, integrated semantic queries. The database is available at https://ppsdb.wikibase.cloud/.