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Friday, December 29, 2017

Using Scholia as Open Notebook Science tool to support literature searching

Source: Compound Interest, Andy Brunning.
CC-BY-ND-NC.
I have blogged about Scholia and the underlying Wikidata before. Following the example of this WikiProject Zika Corpus I am using Scholia (doi:10.1007/978-3-319-70407-4_36, or in Scholia, of course :) as a tool to support a literature study, to collect articles about a certain topic. Previously I used it to track the publication trail around the Elsevier-SciHub interactions. But when I was linking the Compound Interest infographics for the Advent 2017 series to Wikidata items (aiming to archive them on Zenodo) and ran into the poisonous mistletoe graphics of day 9. In this graphics it mentions the phoratoxins. Sadly, not too much was recorded about that in Wikidata.

So, I did an quick scan of literature (about half an hour, using Google Scholar). I ended up with a few articles about the chemistry of this compound, and as good open scientists I used Wikidata and Scholia as a notebook:


From these papers I found reference to six specific, phoratoxins A-F, for which I subsequently created Wikidata items:


I have a lot to discover about these cyclic peptides and they cannot be found in PubChem or ChemSpider (yet):


The SPARQL I uses is as follows and can be run yourself (note the "edit" link in the left corner of this link):

SELECT ?mol ?molLabel ?InChIKey ?CAS ?ChemSpider ?PubChem_CID WITH {
    SELECT DISTINCT ?mol WHERE {
      ?mol wdt:P31/wdt:P279* wd:Q46995757 .
    } LIMIT 500
  } AS %result
  WHERE {
    INCLUDE %result
    OPTIONAL { ?mol wdt:P235 ?InChIKey }
    OPTIONAL { ?mol wdt:P231 ?CAS }
    OPTIONAL { ?mol wdt:P661 ?ChemSpider }
    OPTIONAL { ?mol wdt:P662 ?PubChem_CID }
    SERVICE wikibase:label { bd:serviceParam wikibase:language "en". }
  }

And since I had a few other compound classes there, and in our metabolomics research too, of course, I finally hacked up an extension of Scholia for chemical classes (pull request pending). This is what it looks like for fatty acid:



That makes browsing information about chemicals in Wikidata a lot easier and support our effort to link WikiPathways to Wikidata considerable.

I also used this approach for other topics:

Looking at these pages again, it's great to see the community nature of Wikidata in action. The pages grow in richness over time :)