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Revision as of 15:12, 15 March 2024

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.)

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.

@@ Line 12: / Line 12: @@
 Example entry: [[Item:Q22|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 [[Item:Q56|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 [[Item:Q22|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.