Two Apache Jena SPARQL query performance observations

3 minute read

New Paper: "Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources"

Andra Waagmeester published a paper on his work on a semantic web version of the WikiPathways (doi:10.1371/journal.pcbi.1004989). The paper outlines the design decisions, shows the SPARQL endpoint, and several examples SPARQL queries. These include federates queries, like a mashup with DisGeNET (doi:10.1093/database/bav028) and EMBL-EBI’s Expression Atlas. That results in nice visualisations like this: 2 minute read

Migrating pKa data from DrugMet to Wikidata

In 2010 Samuel Lampa and I started a pet project: collecting pKa data: he was working on RDF extension of MediaWiki and I like consuming RDF data. We started DrugMet. When you read this post, this MediaWiki installation may already be down, which is why I am migrating the data to Wikidata. Why? Because data curation takes effort, I like to play with Wikidata (see this H2020 proposal by Daniel Mietchen et al.), I like Open Data, and it still much needed. 3 minute read

Adding disclosures to Wikidata with Bioclipse

Last week the huge, bi-annual ACS meeting took place (#ACSSanDiego), during which commonly new drug (leads) are disclosed. This time too, like this one tweeted by Bethany Halford: 2 minute read

Adding chemical compounds to Wikidata

Adding chemical compounds to Wikidata is not difficult. You can store the chemical formula (P274), (canonical) SMILES (P233), InChIKey (P235) (and InChI (P234), of course), as well various database identifiers (see what I wrote about that here ]). It also allows storing of the provenance, and has predicates for that too. 2 minute read

New Edition! Getting CAS registry numbers out of WikiData

Source: Wikipedia. CC-BY-SA April this year I blogged about an important SPARQL query for many chemists: getting CAS registry numbers from Wikidata. This is relevant for two reasons: 1 minute read

Coding an OWL ontology in HTML5 and RDFa

There are many fancy tools to edit ontologies. I like simple editors, like nano. And like any hacker, I can hack OWL ontologies in nano. The hacking implies OWL was never meant to be hacked on a simple text editor; I am not sure that is really true. Anyways, HTML5 and RDFa will do fine, and here is a brief write up. This post will not cover the basics of RDFa and does assume you already know how triples work. If not, read this RDFa primer first. 3 minute read