This repository contains an export of interaction data from the Protist-Prokaryote Symbiosis Database for integration with Global Biotic Interactions (GloBI, http://globalbioticinteractions.org).
PPSDB documents symbiotic interactions between protists (microbial eukaryotes) and prokaryotes (bacteria and archaea), with a focus on mutualisms and symbioses with a few specific partners that are in close physical association (endosymbioses, ectosymbioses). Fungi and macroalgae are generally not included, nor are microbiome studies that look at associated microbial communities collectively.
Interaction statements have been manually compiled from the literature. Taxa are linked to the NCBI Taxonomy identifiers where possible.
The original database is structured as linked open data on a Wikibase instance
hosted by Wikibase.cloud. For integration to
GloBI, a subset of the statements are exported in a tabular format (TSV) and
version-controlled in this repository. The export is performed through a SPARQL
query, via a Python script execute_query.py. The dependencies for the Python
script are listed in requirements.txt.
If you have comments or questions please open an issue. Suggestions for new examples to add to the database are particularly welcome.
You are also welcome to browse the original database, which can be searched with SPARQL queries. Please refer to the main site for complete documentation.
The table interactions.tsv contains the list of symbiotic interactions.
Fields follow the guidelines in the GloBI template
repository.