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Introduction

This project aims to describe symbiotic interactions between protists and prokaryotes as structured data.

Envisioned use cases include:

• Search and browse symbiotic interactions by biological taxonomy, leveraging cross-references to external taxonomies (e.g. NCBI Taxonomy, Catalogue of Life)
• Find interactions that are described in earlier literature but not yet studied with modern methods
• Programatically find new literature to update the database, by querying the NCBI databases using linked NCBI taxon IDs
• Share data with GloBI through periodic data exports

Interactions are described with the following statements, roughly aligned with the GloBI terms:

• Taxonomy of 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

This project originated as part of my doctoral dissertation (2017).

Explore the data

View this entry as an example of how the data are modelled: Parduczia sp. ("brown ciliate" of Beinart et al.)

Use the Query Service (link on menu bar) to launch SPARQL queries; have a look at some of the example queries to get started.

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.