In Weekly Report 10 I talked about searching for answers to the question "What height does a grown Pinus sylvestris normally have?". In the post, I looked at some of the articles returned by the query "Pinus sylvestris"[Abstract] AND height, and found interesting information in the tables. The next step was to extract this information. So that's what I did.
In the last two weeks I've been busy with making Version 0.2 of Citation.js. Here I'll explain some of the changes and the reasoning behind them. In the past months I've updated Citation.js several times, and the changes included a Node.js program for the commandline and better Wikidata input parsing. While I was working with the "old" code, I noticed some annoying issues in it. One of the biggest things was the internal data format.
Earlier this week, tarrow published factvis, short for fact visualisation. I decided to have a go with the design, and I made this, in the style of cardlists. Note: If my version and tarrow's version of factvis look very similar, my changes are probably pushed to the master branch already. Screenshot of my factvis design The facts being visualised come from the ContentMine.
When developing Citation.js, I needed to get a JavaScript Object from a string representing one. There are several methods for this, and the one that comes to mind first is JSON.parse(). However, this didn't work.
Last week I made Citation.js usable for the command line, with Node.js. First of all, the main file determines if it is being run with Node.js or in the browser, and switches to Browser or Nodejs mode based on that.
This week I wanted to extend my program, with the lists of cards containing information. In the past few weeks, I made examples with topics such as conifers and zika. In the previous report I explained how I got the facts, and how other people could get them as well. But I felt it was a bit too complex, and mainly too messy.
Last week I wanted to look into extracting more facts, and the relation between found species and compounds. This would be done by extending ami. However, it became clear there will be big improvements to ami in the future, and things like ChemicalTagger and OSCAR are planned to be implemented anyway. It's better to wait for those things to complete before extending it for my own purposes. Instead I improved the card page for future use.
This weekly report covers the past two weeks. I blogged twice last week, and I figured that was enough. Last week I blogged about word clouds from ContentMine output. I also blogged about ctj. This week, I have combined both into interactive lists, as seen here and in the images below. List overview. From left to right: articles, and genus/genera and species that were mentioned in the articles. Search results.
Continuation of this post. I got an answer quite quickly (but after posting the previous post): The Plant List marks what species are in what genus and family, and groups families in Major Groups, e.g. gymnosperms. It also marks synonyms. With a list of conifer species and the ContentMine output, I can determine which species are not conifers, and find how they interact with each other.
Yesterday I published a blogpost, where I talked about ctj and how and why to convert ContentMine's CProjects to JSON. At the end, I mentioned this post, where I would talk about how to use it in different programs, and with d3.js. So here we go. For starters, let's make the data about word frequencies look nice. Not readable (then we would use a table), but visually pleasing. Let's make a word cloud.
