Rogue Scholar Posts

language
Published in chem-bla-ics

Noting that in the coming week I am not attending the ELIXIR All Hands in Uppsala. Having lived in (and around) Uppsala for more than three years, I am disappointed and with the first stories from colleagues coming in even more. But it has been a way too busy year, I have much to finish up, and I need to take care of myself too. I am not 32 anymore. But in the past two weeks I did attend two workshops.

Published in FAIR Data Digest

Hi everyone, in today’s slightly more technical edition I will focus on my recent encounters with the Linked Data query language SPARQL. Many of you may know it as a language to retrieve data (possibly from Wikidata). I mainly use it for a project where I recently found some performance issues that could be resolved by either rewriting the query or changing the approach.

Published in FAIR Data Digest

Hi everyone, this week it’s all about hands-on! I will talk about a webinar on trying to fix quality issues in Wikidata by using its ontology. Additionally I will share a few resources around basics and advanced uses of the query language SPARQL that is used to query Linked Data, for example from Wikidata.

Published in iPhylo

I've released a very crude GraphQL endpoint for WikiData. More precisely, the endpoint is for a subset of the entities that are of interest to WikiCite, such as scholarly articles, people, and journals. There is a crude demo at https://wikicite-graphql.herokuapp.com. The endpoint itself is at https://wikicite-graphql.herokuapp.com/gql.php.

Published in iPhylo

This week I attended the SWAT4(HC)LS (Semantic Web Applications and Tools for Healthcare and Life Sciences) meeting in Edinburgh. Although a relatively small meeting, SWAT4(HC)LS attracts some big names in the field and featured keynotes by Denny Vrandečić (founder of Wikidata), Dov Greenbaum, Birgitta König-Ries, and Helen Parkinson.

Published in iPhylo

In the spirit of release early and release often, here is the first workable version of a biodiversity knowledge graph that I've been working on for Australian animals (for some background on knowledge graphs see Towards a biodiversity knowledge graph now in RIO). The core of this knowledge graph is a classification of animals from the Atlas of Living Australia (ALA) combined with data on taxonomic names and publications from the Australian

Published in iPhylo

For my own use more than anything else I've started creating a list of Wikidata SPARQL queries here. I personally don't find Wikidata's data model particularly easy to grasp, so one way to learn is to take the example queries on the Wikidata Query site and mess about with them. For those interested in taxonomic data Wikidata is quite rich in content.

Published in iPhylo

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.