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Introduction
This project aims to describe symbiotic interactions between protists and prokaryotes as Linked Open Data. Information in the database is compiled from the scientific literature; ~700 symbiotic interactions described in ~380 scientific publications are represented at present. The database is hosted on Wikibase Cloud, a hosting service for Wikibase instances provided by Wikimedia Deutschland.
What can the database be used for?
- Search and browse symbiotic interactions by biological taxonomy, leveraging cross-references to external taxonomies and databases
- Find interactions that were described in earlier literature but not yet studied with modern methods
- Programatically find sequence data, literature, etc. by querying the NCBI databases using linked NCBI taxon IDs
- Share data to be indexed in GloBI, through periodic data exports
Documentation of the workflow and project administration is linked from Project:Main. Your questions may be answered at Project:Q&A
Updates
- 2024-09-21 : Addshore, the original developer of the precursor to Wikibase.cloud (WBStack), wrote a blog post reflecting on the past two years since the project was transferred to Wikimedia Deutschland. I contributed a short user testimonial.
- 2024-08-26 : Released a preprint manuscript describing the database motivation and design, intended for biologists who may use the database or want to build similar projects
Explore the data
Some example entries to see how the data are modeled:
- Parduczia sp. from Santa Barbara Basin ("brown ciliate"), a marine ciliate
- Pelomyxa palustris, a freshwater amoebozoan
- Mixotricha paradoxa, itself a hint gut symbiont of the termite Mastotermes darwiniensis
- Candidatus Megaira polyxenophila, a bacterial endosymbiont of a diverse array of protists and algae
Each interaction statement is supported by one or more references to the scientific literature, linked by their DOI if available.
Entities (e.g. taxa, publications) can be found by a free-text search of their labels with the search bar (top of each page) or at Special:Search.
Semantic queries, which make use of the data model (e.g. "find host species where symbionts are Alphaproteobacteria"), require the use of the SPARQL query language. Use the Query Service (link on menu bar) to launch SPARQL queries; try the example queries to get started.
Data linking
We wish to capture different facets of symbiotic interactions, and link these to other databases and ontologies.
| Information | Relevant database or ontology |
|---|---|
| Taxonomy of interacting organisms | NCBI Taxonomy, Wikidata |
| Localization of symbionts in host organism | Gene Ontology, Uberon |
| Nature of biotic interactions, if known/inferred | Relation Ontology |
| Analytical methods used to identify organisms or interaction type | OBI, Evidence Ontology |
| Environment where organisms were isolated | Environment Ontology |
| Representative SSU rRNA or genome sequences | Genbank |
| Scientific publications describing symbiosis | DOI, Wikidata |
Terms will be linked to other linked open data or ontologies, if there is a suitable exact match. The EMBL-EBI Ontology Lookup Service is a useful resource for browsing life science related ontologies.
Links
This project originated as part of my doctoral dissertation (2017).
Similar projects elsewhere:
- Global Biotic Interactions (GloBI) (Poelen et al., 2014) an aggregator for biotic interactions datasets across all domains of life
- Protist Interaction Database (PIDA) (Bjorbækmo et al., 2019) (last updated 2018)
- Diatom Interaction Database (DIDB) (Vincent & Bowler, 2020) (last updated 2019)
- AQUASYMBIO (last updated 2017)