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Posts uit november, 2017 tonen

Wikidata&Amino-acids

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Yesterday I have been working on annotating a data set, which contained lots of amino acids. For this annotation I made use of the Wikidata database. The fun thing with this database, is that it is very structured. You can do for example SPARQL queries on it (and even though I wasn't familiar with these before I started my PhD, I rather enjoy them now). Below is an example query, which gives all proteinogenic coding L-amino acids (so the active forms of the amino acids, which are being build into proteins through transcription). SELECT ?ID ?IDLabel  WHERE  {    ?ID wdt:P279 wd:Q8066 .    ?ID wdt:P279 wd:Q24301658 .    ?ID wdt:P279 wd:Q3241589 .    SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }  } This gave me 19 results (in 244 ms), and to my surprise there was a mistake in the results: D-isoleucine was labeled as an L-amino acid. So I went in Wikidata again and fixed this issue (which was quit easy since the result from the