![\"\"](\"/assets/images/pKa.png\")
In 2010 Samuel Lampa and I started a pet project:\ncollecting pKa data: he was working on RDF extension of MediaWiki and I like consuming\nRDF data. We started DrugMet.\nWhen you read this post, this MediaWiki installation may already be down, which\nis why I am migrating the data to Wikidata.\nWhy? Because data curation takes effort, I like to play with Wikidata (see\nthis H2020 proposal by \nDaniel Mietchen et al.), I like Open Data, and it still\nmuch needed.
\n\nWe opted for a page with the minimal amount of information. To maximize the speed\nat which we could add information. However, when it came to semantics, we tried\nto be as explicit as possible, and, e.g. use the CHEMINF ontology.\nSo, it collected:
\n\nA page typically looks something like this:
\n\n
While not used on all pages, at some point I even started using templates, and\nI used these two, for molecules and papers:
\n\n{{Molecule\n |Name=\n |InChIKey=\n |DOI=\n |Wikidata=\n}}\n\n{{Paper\n |DOI=\n |Year=\n |Wikidata=\n}}\nThese templates, as well as the above screenshot, already contain a spoiler, but\nmore about that later. Using MediaWiki functionality it was now easy to make lists,\ne.g. for all pKa data (more spoilers):
\n\n![\"\"](\"/assets/images/pKa1.png\")
I find a database like this very important. It does not capture all the information\nit should be capturing, though, as is clear from the proposal\nsome of use worked on a while back. However, this project got on hold; I don’t\nhave time for it anymore, and it is not core to our department enough to spend\ntime on write grant proposals for it.
\n\nBut I still do not want to get this data get lost. Wikidata is something I have\nstarted using, as it is a machine readable CCZero database with an increasing\namount of scientific knowledge. More and more people are working on it, and you\nmust absolutely read this paper\nabout this very topic (by a great team\nyou should track, anyway). I am using it myself as source of identifier mappings\nand more. So, migrating the previously collected data to Wikidata makes perfect\nsense to me:
\n\nI can annotate data with the data source (paper) it came from and also experimental conditions:
\n\n![\"\"](\"/assets/images/pKa2.png\")
In fact, you’ll note that the the book is a separate Wikidata entry in itself.\nBetter even, it’s an ‘edition’ of the book. This is the whole point we make in\nthe above linked H2020 proposal: Wikidata is not a database specific for one\ndomain, it works for any (scholarly) domain, and seamlessly links all those\ndomains.
\n\nNow, to keep track of what data I have migrated, I am annotating DrugMet entries\nwith links to Wikidata: everything with a Wikidata Q-code is already migrated.\nThe above pKa table already shows Q-identifiers, but I also created them for all\ndata sources I have used (three of them are two books and\none old paper without a DOI):
\n\n![\"\"](\"/assets/images/pKa3.png\")
I have still quite a number of entries to do, but all the protocols are set up now.
\n\nOn the downstream side, Wikidata is also great because of\ntheir SPARQL end point. Something that I did not\nget worked out some weeks ago, I did manage yesterday (after\nsome encouragement from @arthursmith):\nlist all pKa statements, including literature source if available:
\n\nIf you run that query on the Wikidata endpoint,\nyou get a table like this:
\n\n![\"\"](\"/assets/images/pKa4.png\")
We here see experimental data from two papers: 10.1021/ja01489a008\nand 10.1021/ed050p510. This can all be\ndisplayed a lot fancier, like make histograms, tables with 2D drawings of the\nchemical structures, etc, but I leave that to the reader.
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