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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 | : 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. | ||
: Therefore, the item "brown ciliate" is modeled here as a provisional taxon, because it does not have an exact equivalent in the NCBI Taxonomy. | |||
: For [[Item:Q301|Q301]], an SSU rRNA sequence has been published. The property [[Property:P28|P28]] is used to link to a representative sequence for disambiguation. | |||
; 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. | ||