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== Q & A ==
== Q & A ==
 
; Which types of interactions are in the scope of this database?
: Interactions between protists (microbial eukaryotes) and prokaryotes (bacteria and archaea). In a few cases, interactions between two eukaryotic partners, or interactions with viruses, may also be included if they occur in organisms that also participate in protist-prokaryote interactions.
: Fungi and macroalgae are generally not included, as are microbiome studies. Reports of putative symbionts described solely by morphology without further phylogenetic characterization may be included if the host organism is somehow notable, or if they are in older literature about host taxa that have not yet been studied with modern methods.
; Why use a single 'interacts with' statement, with qualifiers for interaction type, instead of different properties for each interaction type?
; 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
: The 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 an environmental "ciliate metagenome" identifier on NCBI that is used for convenience to organize records comprising sequences from multiple taxa, rather than a legitimate taxon in the biological sense.
: Therefore, the item "brown ciliate" is described here as a placeholder taxon, because it does not have an exact equivalent in the NCBI Taxonomy, although we think it represents a legitimate taxon, based on the information in the cited references.
: For [[Item:Q301|Bacteroidales sp. Cc3-010 ectosymbiont of Caduceia versatilis]], an SSU rRNA sequence has been published, but it is currently placed in a provisional "taxon" in the NCBI Taxonomy that is again a convenience label for records where taxonomic information is lacking. The property [[Property:P28|P28]] is used to link our placeholder taxon to a representative sequence from the cited reference, for disambiguation should the NCBI Taxonomy be updated in the future.
; Why do some interacts with statements link to "unknown value"?
: If a symbiont is reported only on the basis of microscopy, without any information on its phylogenetic affiliation, "unknown value" is used for the object of the statement.
: If some information is known about its likely taxonomy, e.g. through use of group-specific FISH probes, then a placeholder taxon is created with a temporary name.
: The entry [[Item:Q448|''Metopus contortus'']] has both an "unknown value" statement and a placeholder symbiont taxon [[Item:Q442|Q442]].
; Why host this on Wikibase?
; Why host this on Wikibase?
: This database has seen a number of iterations: starting as a table in a word processor file, to spreadsheets, a custom SQLite database, and an attempt to homebrew a structured data base with XML files and Python scripts. After getting some experience on Wikidata, I found that Wikibase offers the key features that I wanted: flexible and extensible schemata, graphical frontend for manual data entry, options for programmatic data import from tables, integration with external databases, and a sophisticated query interface.
: This database has seen a number of iterations: starting as a table in a word processor file, to spreadsheets, a custom SQLite database, and an attempt to homebrew a structured data base with XML files and Python scripts. After getting some experience on Wikidata, I found that Wikibase offers the key features that I wanted: flexible and extensible schemata, graphical frontend for manual data entry, options for programmatic data import from tables, integration with external databases, and a sophisticated query interface.
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: [[Item:Q7|Kentrophoros sp. H]]
: [[Item:Q7|Kentrophoros sp. H]]
: (The logo may not be visible in the mobile version of this site.)
: (The logo may not be visible in the mobile version of this site.)
; Which types of interactions are in the scope of this database?
: Interactions between protists (microbial eukaryotes) and prokaryotes (bacteria and archaea). In a few cases, interactions between two eukaryotic partners, or interactions with viruses, may also be included if they occur in organisms that also participate in protist-prokaryote interactions.
: Fungi and macroalgae are generally not included, as are microbiome studies. Reports of putative symbionts described solely by morphology without further phylogenetic characterization may be included if the host organism is somehow notable, or if they are in older literature about host taxa that have not yet been studied with modern methods.
Retrieved from "https://ppsdb.wikibase.cloud/wiki/Special:MobileDiff/11631"

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