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:: Example: ''Candidatus'' Megaira polyxenophila is a bacterium that has been described in the scientific literature, and given a provisional ("Candidatus") name at the species level. An NCBI taxon ID has been assigned to this taxon name, which corresponds to the taxon concept from the literature. | :: Example: ''Candidatus'' Megaira polyxenophila is a bacterium that has been described in the scientific literature, and given a provisional ("Candidatus") name at the species level. An NCBI taxon ID has been assigned to this taxon name, which corresponds to the taxon concept from the literature. | ||
:: In this database, such items are encoded as instances of the class "taxon". | :: In this database, such items are encoded as instances of the class "taxon". | ||
:: In some cases, a taxon concept has been assigned a different name in the publication from the name that appears in the NCBI Taxonomy record. This usually happens when a sequence was first published in NCBI under a temporary name, which has not been updated with the subsequent formal name. These are nonetheless encoded here as "taxon" items, but are additionally tagged as [[Item:Q658|"NCBI taxon name needs updating"]]. Example: [[Item:Q2018|''Candidatus'' Vesiculincola pelomyxae]] is still listed under a provisional name "Eubacteriales bacterium SKADARSKE-1" in the NCBI Taxonomy, but the provisional name is clearly unique and refers to the same taxon entity as the published name. | |||
:; 2. The taxon name/concept in the original publication does not correspond exactly to the NCBI taxon, but sequence data are available. | :; 2. The taxon name/concept in the original publication does not correspond exactly to the NCBI taxon, but sequence data are available. | ||
:: Example: The ciliate species [[Item:Q52|''Eufolliculina methanicola'']] was described and named in a scientific publication, but sequences from that study were published under a non-specific identifier "Folluculinidae sp." in the NCBI Taxonomy, that potentially represents sequences from multiple taxa. | :: Example: The ciliate species [[Item:Q52|''Eufolliculina methanicola'']] was described and named in a scientific publication, but sequences from that study were published under a non-specific identifier "Folluculinidae sp." in the NCBI Taxonomy, that potentially represents sequences from multiple taxa. | ||
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: Where possible, taxon items are linked to their corresponding NCBI taxon ID and/or Wikidata item, so they can be placed into the context of either the NCBI Taxonomy or the Wikidata taxonomy trees. | : Where possible, taxon items are linked to their corresponding NCBI taxon ID and/or Wikidata item, so they can be placed into the context of either the NCBI Taxonomy or the Wikidata taxonomy trees. | ||
: However, not all taxa have corresponding NCBI taxon IDs or Wikidata items. In some cases ("placeholder taxon"), the NCBI Taxonomy may be inconsistent with the published literature or not yet updated. In other cases ("named organism without published sequence data"), there is information about their taxonomy, but sequence data are not available. Or the taxon may not meet the notability criteria for inclusion in the Wikidata database (e.g. strains or species that have not been formally named). | : However, not all taxa have corresponding NCBI taxon IDs or Wikidata items. In some cases ("placeholder taxon"), the NCBI Taxonomy may be inconsistent with the published literature or not yet updated. In other cases ("named organism without published sequence data"), there is information about their taxonomy, but sequence data are not available. Or the taxon may not meet the notability criteria for inclusion in the Wikidata database (e.g. strains or species that have not been formally named). | ||
: Therefore, every taxon item is linked to its next highest parent taxon. The parent taxon item is linked to Wikidata. This allows us to query the database taxonomically using the Wikidata taxonomy tree, with a [[Project:SPARQL/examples#Find_interactions_where_symbiont_is_member_of_Alphaproteobacteria_according_to_Wikidata|federated SPARQL query]]. | : Therefore, every taxon item is linked to its next highest formally named parent taxon. The parent taxon item is linked to Wikidata. This allows us to query the database taxonomically using the Wikidata taxonomy tree, with a [[Project:SPARQL/examples#Find_interactions_where_symbiont_is_member_of_Alphaproteobacteria_according_to_Wikidata|federated SPARQL query]], even for taxon items that are not represented in external databases. | ||
: The parent taxon items are instances of the class "higher taxon" and should not be used for "interacts with" statements. | : The parent taxon items are instances of the class "higher taxon" and should not be used for "interacts with" statements. | ||