University of Glasgow

Roderic Page

![Sahelanthropus tchadensis TM 266 01 060
1](https://lh3.googleusercontent.com/-KHYSH_cNTOY/WHoQ2AHLlSI/AAAAAAAAEXQ/lGNjPer4Qno/Sahelanthropus_tchadensis_-_TM_266-01-060-1.jpg?imgmax=1600 "Sahelanthropus_tchadensis_-_TM_266-01-060-1.jpg"){border="0"
width="128" height="107" style="float:right;"} Following on from
previous posts [The Semantic Web made fun:
d3sparql](http://iphylo.blogspot.com/2016/11/the-semantic-web-made-fun-d3sparql.html)
and [The Biodiversity Heritage Library meets Wikidata via Wikispecies:
adding author identifiers to
BioStor](http://iphylo.blogspot.com/2017/01/the-biodiversity-heritage-library-meets.html)
I\'ve put together an example query that can be used to extract a
taxonomic classification from Wikidata. The query is inspired by the
<http://biohackathon.org/d3sparql/> example, and uses the wikidata
property [P171](https://www.wikidata.org/wiki/Property:P171) (\"parent
taxon\") which is subproperty of rdfs:subClassOf (the property used in
the d3sparql example which queries the Uniprot taxonomy).

The following SPARQL query generates a list of nodes in the tree
representing the classification of
[Hominini](https://en.wikipedia.org/wiki/Hominini) (humans, chimps, and
their extinct relatives):

    PREFIX wdt: 
    PREFIX wd: 
    SELECT ?root_name ?parent_name ?child_name WHERE
    {
     VALUES ?root_name {"Hominini"}
     ?root wdt:P225 ?root_name .
     ?child wdt:P171+ ?root .
     ?child wdt:P171 ?parent .
     ?child wdt:P225 ?child_name .
     ?parent wdt:P225 ?parent_name .
    }

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Using https://query.wikidata.org/sparql as the endpoint, in
<http://biohackathon.org/d3sparql/> this generates the following
diagram:

![Screenshot 2017 01 14 11 41
55](https://lh3.googleusercontent.com/-p1lzN04RdZg/WHoQzuBIeRI/AAAAAAAAEXI/1_gTWxnZ4vo/Screenshot%2525202017-01-14%25252011.41.55.png?imgmax=1600 "Screenshot 2017-01-14 11.41.55.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="460" height="418"}

There are some obvious issues with this classification, such as genera
that lack descendant species (e.g., *Cyphanthropus*). Indeed, we could
imagine developing SPARQL queries to flag up such errors (see [A use
case for RDF in
taxonomy](http://iphylo.blogspot.com/2013/08/a-use-case-for-rdf-in-taxonomy.html)).
But the availability and accessibility of Wikidata and its SPARQL
interface makes it a great playground to explore the utility of SPARQL
for exploring taxonomic data.


Following on from previous posts The Semantic Web made fun: d3sparql and The Biodiversity Heritage Library meets Wikidata via Wikispecies: adding author identifiers to BioStor I've put together an example query that can be used to extract a taxonomic classification from Wikidata.

Messaggi di Rogue Scholar

Displaying taxonomic classifications from Wikidata using d3js and SPARQL