Just a small blog before the weekend starts... Since I guided a student from the Forensic Science Master (University of Amsterdam) during her literature thesis on Volatile Organic Compounds from narcotics in breath (presenting her findings on Dec. 13th of 2017, 13:45-14.30, Location A1.06), I wanted to investigate how much information I can find on narcotics in Wikidata . However, there was no label to investigate which compounds are listed under the Opium law (Dutch law on prohibited substance, which you are allowed to use, but not to sell/traffic etc.). So, I added this label for the compounds from List 1 and 2 (there is a difference in harm, however all compounds on these lists are considered to be narcotics), where there was a International Non-proprietary Name (INN) listed (Note: I hope to get to the compounds which do not have an INN yet somewhere in the near future). So, after I did all this manual work (261 unique chemical compounds), I wanted to see what I could do with all...

New day, new blog. Since I like the visualisation of the bubble chart from Wikidata, I tried to see what else I could do with it. This time, I am looking at all chemical compounds, which physically interact with another compound (which was an idea that I got after reading an interesting paper on Key characteristics of Carcinogenics ). When I do this for all chemical compounds in Wikidata, I get the following visualisation (click on the link for a direct visualisation [query 1]): http://tinyurl.com/y9vef38n Looks like a big hairball of information to me; so I narrowed down the search results to metabolites which are present in Wikipathways (click on the link for a direct visualisation [query 2]): http://tinyurl.com/ybmkaazc So, I think that we are doing all right in WikiPathways concerning metabolites which physically interact with another one; however it would be nice if I could include how these compounds interact with each other (agonist/antagonist) and group according...

From the previous blog it was apparent that Wikidata could use some additional information concerning amino acids. I added some content, for example which triplet codes for which amino acid (the active L-forms only) and which amino acids are considered to be essential (and have to be taking in via diet). There are also amino acids which are considered to be dispensable in the human body, and are therefore synthesised in the body itself. I wondered in which pathways I could find these non-essential amino acids and did a query on it in Wikidata: SELECT ?ID ?IDLabel (COUNT(DISTINCT ?PWID) AS ?count) WHERE{  ?ID wdt:P279 wd:Q8066 .  ?ID wdt:P279 wd:Q44266770 .   ?PWID wdt:P31 wd:Q4915012 .   ?PWID wdt:P527 ?ID .     SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". } } GROUP BY ?ID ?IDLabel ORDER BY DESC(?count) This revealed that there are 5 non essential amino acids, however only 4 can be found in mu...