Database Release: PPSDB, a Linked Open Data Knowledge Base for Protist-Prokaryote Symbioses

Area of Science:

• Microbiology
• Eukaryotic Biology
• Symbiosis Research

Background:

• Symbiotic interactions between protists (microbial eukaryotes) and prokaryotes (bacteria and archaea) are crucial for ecological and evolutionary processes.
• A comprehensive overview of the diversity and literature on these interactions is challenging to maintain.

Purpose of the Study:

• To present the Protist-Prokaryote Symbiosis Database (PPSDB), a manually curated knowledge base.
• To address challenges in managing and accessing data on protist-prokaryote symbiosis.

Main Methods:

• Manual curation of 1146 interaction statements from 443 publications.
• Annotation of biological taxonomy, anatomical localization, and analytical methods.
• Mapping data to external databases and ontologies (e.g., Wikidata, NCBI Taxonomy, Gene Ontology).
• Development of a data model to handle incomplete information and inconsistent taxon concepts.
• Utilizing a Wikibase software platform for extensibility and programmatic access.

Main Results:

• The PPSDB contains 1146 curated interaction statements.
• The database integrates taxonomic, localization, and methodological data.
• The data model and platform are designed to handle data inconsistencies and are extensible.
• The database enables programmatic access and semantic queries.

Conclusions:

• The PPSDB provides a structured, queryable knowledge base for protist-prokaryote symbiosis.
• The database design offers a model for similar data integration projects.
• PPSDB facilitates a deeper understanding of microbial symbiotic interactions.