Physical interactions of compounds

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 to these roles. I will try that later hopefully.

If you want to try these visualisations out yourself, check the queries below:

[query 1]:

#defaultView:BubbleChart

SELECT ?ID ?IDLabel (COUNT(DISTINCT ?interaction) AS ?count) #?interactiontype

WHERE{

  ?ID wdt:P31 wd:Q11173.

  ?ID wdt:P129 ?interaction .

 # ?interaction wdt:P2868 ?interactiontype. has to work for interaction type as well!!

SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }

}

GROUP BY ?ID ?IDLabel

ORDER BY DESC(?count) ASC(?IDLabel)

[query 2]:

#defaultView:BubbleChart

SELECT ?ID ?IDLabel (COUNT(DISTINCT ?interaction) AS ?count) #?interactiontype

WHERE{

  ?ID wdt:P31 wd:Q11173.

  ?ID wdt:P129 ?interaction .

  

 ?PWID wdt:P31 wd:Q4915012 . 

 ?PWID wdt:P527 ?ID . 

  

  # ?interaction wdt:P2868 ?interactiontype. has to work for interaction type as well!!

SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }

}

GROUP BY ?ID ?IDLabel

ORDER BY DESC(?count) ASC(?IDLabel)