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Introduction
Symbiotic interactions between protists and prokaryotes, described with structured data.
The aim is to model information about:
- Taxonomy of both hosts and symbionts, with links to external databases (primarily NCBI)
- Localization of symbionts in cellular compartments of the host cell, using Gene Ontology terms
- Nature of biotic interactions, if this is known, using Relation Ontology terms (although there are some limitations in this ontology for describing mutualistic interactions)
- Analytical methods used to study the symbioses
The information was originally collected as part of my doctoral dissertation (2017).
Example entry: Parduczia sp. ("brown ciliate" of Beinart et al.)
Q & A
- Why use a single 'interacts with' statement, with qualifiers for interaction type, instead of different properties for each interaction type?
- Nature of an interaction is often not fully understood, or may have multiple facets. Coding interaction types as qualifiers allows us to stack multiple functional roles on a single interaction
- What is a placeholder taxon?
- We would like to model taxonomic relationships ("find taxa that are members of Ciliophora") and also link out to external databases, particularly NCBI. However, there is often a discrepancy between NCBI Taxonomy and the "actual" taxonomy.
- For example, the brown ciliate is reported as a Parduczia sp. based on sequence analysis, but the sequences from that study are published under a placeholder "ciliate metagenome" identifier on NCBI.