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; What is a [[Item:Q56|placeholder taxon]]? | ; 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. | : 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. | : 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 | : 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. The property [[Property:P28|P28]] is used to link to a representative sequence for disambiguation. | : 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"? | ; 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 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. | ||