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Saturday, September 09, 2017

New paper: "RDFIO: extending Semantic MediaWiki for interoperable biomedical data management"

Figure 10 from the article showing what the DrugMet wiki
with the pKa data looked like. CC-BY.
When I was still doing research at Uppsala University, I had a internship student, Samuel Lampa, who did wonderful work on knowledge representation and logic (check his thesis). In that same period he started RDFIO, a Semantic MediaWiki extension to provide a SPARQL end point and some clever feature to import and export RDF. As I was already using RDF in my research, and wikis are great way to explore how to model domain data, particularly when extracted from diverse literature, I was quite interested. Together we worked on capturing pKa data, and Samuel had put DrugMet online. Extracting pKa values from primary literature is a lot of laborious work and crowdsourcing did not pick up. This data was migrated to Wikidata about a year ago.

I also used the RDFIO extension when I started capturing nanosafety data from literature when I worked at Karolinska Institutet. I will soon write up this work, as the NanoWiki (check out these FigShare data releases) was a seminal data set in eNanoMapper, during which I continued adding data to test new AMBIT features.

Earlier this week Samuel's write up of his RDFIO project was published, to which I contributed the pKa use case (doi:10.1186/s13326-017-0136-y). There are various ways to install the software, as described on the RDFIO project site. The DrugMet data as well as the data for the OrphaNet data from the other example use case can also be downloaded from that site.

Lampa, S., Willighagen, E., Kohonen, P., King, A., Vrandečić, D., Grafström, R., & Spjuth, O. (2017). RDFIO: extending semantic MediaWiki for interoperable biomedical data management. Journal of Biomedical Semantics, 8 (1). http://dx.doi.org/10.1186/s13326-017-0136-y