Saturday, February 17, 2018

FAIR-er Compound Interest Christmas Advent 2017: learnability and citability

Compound Interest infographics
of yesterday.
I love Compound Interest! I love what it does for popularization of the chemistry in our daily life. I love that the infographics have a pretty liberal license.

But I also wish they would be more usable. That is, the usability is greatly diminished by the lack of learnability. Of course, there is not a lot of room to give pointers.  Second, they do not have DOIs and are hard to cite as source. That said, the lack of sourcing information may not make it the best source, but let's consider these aspects separate. I would also love to see the ND clause got dropped, as it makes it harder to translate these infographics (you do not have that legal permission to do so) and fixing small glitches has to involve Andy Brunning personally.

The latter I cannot change, but the license allows me to reshare the graphics. I contacted Andy and proposed something I wanted to try. This post details some of the outcomes of that.

Improving the citability
This turns out to be the easy part, thanks to the great integration of GitHub and Zenodo. So, I just started a GitHub repository, added the proper license, and copied in the graphics. I wrapped it with some Markdown, taking advantage of another cool GitHub feature, and got this simple webpage:

By making the result a release, it got automatically archived on Zenodo. Now Andy's Compound Interest Christmas Advent 2017 has a DOI: 10.5281/zenodo.1164788:

So, this archive can be cited as:
    Andy Brunning, & Egon Willighagen. (2018, February 2). egonw/ci-advent-2017: Compound Interest Christmas Advent 2017 - Version 1 (Version v1). Zenodo.
Clearly, my contribution is just the archiving and, well, what I did as explained in the next section. The real work is done by Andy Brunning, of course!

Improving the learnability
One of the reasons I love the graphics, it that is shows the chemicals around is. Just look aside your window and you'll see the chemicals that make flowers turn colorful, berries taste well, and several plants poisonous. Really, just look outside! You see them now? (BTW, forget about that nanopores and minions, I want my portable metabolomics platform :)

But if I want to learn more about those chemicals (what are their properties, how do I extract them from the plants, how will I recognize them, what toxins are I (deliberately, but in very low doses) eating during lunch, who discovered them, etc, etc?), those infographics don't help me.

Scholia to the rescue (see doi:10.1007/978-3-319-70407-4_36): using Wikidata (and SPARQL queries) this can tell me a lot about chemicals, and there is a good community that cares about the above questions too, and adds information to Wikidata. Make sure to check out WikiProject Chemistry. All it needed is a Scholia extension for chemicals, something we've been working on. For example, check out bornyl acetate (from Day 2: Christmas tree aroma):

This list of identifiers is perhaps not the most interesting, and we're still working out how we can make it properly link out with the current code. Also, this compound is not so interesting for properties, but if there is enough information, it can look list this (for acetic acid):

I can recommend exploring the information it provides, and note the links to literature (which may include primary literature, though not in this screenshot).

But I underestimated the situation, as Compound Interest actually includes quite a few compound classes, and I had yet to develop a Scholia aspect for that. Fortunately, I got that finished too (and I love it), and it as distinct features and properly integrated, but to give you some idea, here is what phoratoxin (see Day 9: Poisonous Mistletoe) looks like:

Well, I'm sure it will look quite different in a year from now, but I hope you can see where this is going. It is essential we improve the FAIR-ness (see doi:10.1038/sdata.2016.18) of resources, small and large. If project like Compound Interest would set an example, this will show the next generation scientists how to do science better.