One key feature of programming languages is the following: first, there is linearity. This is an important point that is not always clear to students who just start to program. In fact, ask yourself what the algorithm is for counting the chairs in the room where you are now sitting. Could a computer do that in the same way? How should your algorithm change? A key point is, is that the program is run step by step, in a linear way.

Now that we have the communication working with the Open PHACTS LDA, it is time to make a nice GUI.

The purpose of a web service is that you give it a question or task, and that it returns an answer. For example, we can ask the Open PHACTS platform what compounds it knows with aspirin in the name. We pass the question (with the API key) and get a list of matching compounds. Now, this communication is complex: it happens at many levels, which are spelled out in the Internet Model.

Now that I have wrote out the goals, what they students will practically do, and how to get started with the Open PHACTS platform, I will list how we will assess the students: a presentation on the second day, outlining the project and work plan, working source code at the end of the cour se, a final presentation, showing the results and conclusions. Primarily, they will be judged on their acquired programming skills.

I have outlined the scope of the six-day course: the students will learn to program while hacking on the Open PHACTS’ Linked Data API (LDA). The first step is to get an account for the LDA. I have already done that to save time. But these are the steps to take. You go to https://dev.openphacts.org/signup: You then approve the account via your email account and you are set. The account is needed to get an API key.

Our department will soon start the course Programming in the Life Sciences for a group of some 10 students from the Maastricht Science Programme. This is the first time we give this course, and over the next weeks I will be blogging about this course. First, some information.

Update : Mark wrote up a blog post on the RDF that the ChEMBL team itself. Yesterday, the paper “The ChEMBL database as linked open data” (doi:10.1186/1758-2946-5-23) by Andra Waagmeester (@andrawaag), Ola Spjuth (@ola_spjuth), Peter Ansell (@p_ansell), Antony Williams (@chemconnector), Valery Tkachenko, Janna Hastings, Bin Chen (@binchenindiana), David J Wild (@davidjohnwild), and me appeared in the OA JChemInf journal.

The “Emerging practices for mapping and linking life sciences data using RDF” (doi:10.1016/j.websem.2012.02.003) is now available online, where I contributed a section on the original workflow for creating ChEMBL triples, and contributed to the section about open licensing, referring to CCZero and the Panton Principles. Happy reading!

Update: this work is now described in this paper .

Readers of my blog know I have been using the Citation Typing Ontology, CiTO (doi:10.1186/2041-1480-1-S1-S6). I allows me to see how the CDK is cited and used . CiteULike is currently adding more CiTO more functionality, which they started doing almost one and a half years ago.

Six month was not quite the amount of time I anticipated between the third and fourth edition, but I finally managed to upload edition 1.4.7-0 of my Groovy Cheminformatics book. The first three editions sold 37 copies, including two for myself.