Monday, April 20, 2020

Making sense of how Wikidata models taxonomy

Given my renewed enthusiasm for Wikidata, I'm trying to get my head around the way that Wikidata models biological taxonomy. As a first pass, here's a diagram of the properties linked to a taxonomic name. The model is fairly comprehensive, it includes relationships between names (e.g, basionym, protonym, replacement), between taxa (e.g., parent taxon), and links to the literature. It's also a complex model to query, given that a lot of information is expressed using qualifiers. Hence there's a bit of head scratching while I figure out the relationship between properties, statements, etc.

Links to the literature is one of my interests, can in cases where Wikidata has this information you can start to enhance the way we display publications, e.g.

The Wikidata model is very like that used in Darwin Core, where everything is a taxon and every taxon has a name, which means that relationships that are notionally between names and not taxa (e.g., basionym) are all treated as relationships between taxa.

One big challenge is how to interpret Wikidata as a classification, given that we expect classifications to be trees. The taxonomic classification in Wikidata is clearly not a tree, for example:

What I think is happening here is that different people are adding different parent taxa, depending on which classification they follow. Some classifications (e.g., that used by GBIF) are "shallow" with only a few levels (e.g., kingdom, phylum, class, order, family, genus), other classifications are deep (e.g., NCBI). So the idea of simply being able to do a SPARQL query and get a tree (e.g. Displaying taxonomic classifications from Wikidata using d3js and SPARQL) runs into problems. But this could also be a strength, particularly if we had a reference or source for each parent child pair. That way we could (a) store multiple classifications in Wikidata, and (b) have queries that retreive classifications according to a particular source (e.g., GBIF).

So, lots of potential, but lots I've still to learn.