chem-bla-ics: October 2010

CiteULike CiTO Use Case #1: Wordles

Last month I reported a few things I missed in CiteULike. One of them was support for CiTO (see doi:10.1186/2041-1480-1-S1-S6), a great Citation Typing Ontology.

I promised the CiTO author, David, my use cases, but have been horribly busy in the past few weeks with my new position, wrapping up my past position, and thinking on my position after Cambridge. But finally, here it is. Based on source code I wrote and released earlier, the first use case I represent is the Wordle one, which I showed with manual work in February.

Now that all the data is semantically marked up in CiteULike, I can easily extract all paper titles (or whatever is available in CiteULike) for all papers that cite the first CDK paper (doi:10.1021/ci025584y).

Oct

Calculating molecular descriptors with OpenTox

While working during office hours on Oscar, I am also trying to finish up some work left from Uppsala. One such thing is the Bioclipse-OpenTox project (see Using Bioclipse to upload data to an OpenTox server and Oxford, August 2010: eCheminfo Predictive ADME & Toxicology 2010 Workshop).

Oct

Uninformative Blue Obelisk eXchange notification

This email informing me about a newly earned badge does not seem very

informative.

Oct

Algorithm or Model: OpenTox API quiz

Nina (who still does not seem to blog) wrote up this interesting question, triggered by the OpenTox API ontology:Given: A publication, describing specific method of property prediction (not a generic machine learning algorithm). An implementation of this publication. Example: pKa. This is a decision tree with SMARTS in the nodes. There is a training set, which could be used in validation.

Oct

Oscar4 Java API: chemical name dictionaries

Besides getting Oscar used by ChEBI (hopefully via Taverna), my main task in my three month Oscar project is to refactor things to make it more modular, and remove some features no longer needed (e.g. an automatically created workspace environment). Clearly, I need to define a lot of new unit tests to ensure my assumptions on how to code works are valid.

Oct

CDK 1.2 to 1.4 API changes #2: implicit hydrogens

A second API change lies deep in the IAtom interface. To reflect more accurately the meaning of the method, the IAtomType.getHydrogenCount() has been renamed to IAtomType.getImplicitHydrogenCount(), and likewise the setter methods.

CDK 1.2 code

carbon.setHydrogenCount(4); CDK 1.4 code

carbon.setImplicitHydrogenCount(4); Yeah, that's a simple one. Just to make clear, in both versions the count reflected the number of implicit hydrogens.

Oct

CDK 1.2 to 1.4 API changes #1: creating objects with an IChemObjectBuilder

Later this year (planned) a new stable branch of the CDK library will be released. Time to look at some API changes, to ease migration. In this first post of the series, I will show how the IChemObjectBuilder functionality has changed.

Oct

Multiple unit test inheritance with JExample

Two months ago I wrote about JExample (see Specifying unit test dependencies with JExample). At the time, my examples did not include multiple unit test inheritance, but was informed later by @jexample that is possible.

Oct

Really free chemistry books #2: @bookboon

About a year ago I wrote about free chemistry books. No, not illegal copied books, but really free books (though, not necessarily Open). Actually, the books I discussed last year, those are out of copyright, as they are old. But, just today I ran into an advertisement for free books by bookboon.com (twitter:bookboon), and these are new books.

Oct

The Answer to: Are these organic molecules the same?

Ten days ago I asked my readers if two molecules were the same or not. I guessed they were not, when I was asked Are these organic molecules the same? The people who replied to my post were quite convinced they were, and Peter gave the context of the pub quiz: assumptions may not be correct.

Indeed, I assumed there were hydrogens missing (implicit), and that line corners indicate places where carbons are.