Update : the fourth edition is out. Some project are never finished.

Some time ago, the brilliant GitHub people gave me the following tip. Rajarshi is lazy, and might find it interesting. By appending .patch to the commit URL, a commit can easily be downloaded as patch. That way, developers can easily download it with wget or curl and apply it locally with git am, without having the fetch the full repository.

Later this year the ninth International Conference on Chemical Structures (ICSS) conference will be held in the Netherlands. I had the pleasure of joining this meeting, I think, eight years ago, when I was doing my PhD in Nijmegen. Mind you, I did not attend the conference;

Oscar is a text miner. It mines in text for chemistry. Oscar4 is the next iteration of Oscar code that I worked on in the past three months, with Lezan, Sam, and David.

Mark’s new CCO/RDF hosting functionality (see also my post two days ago) requires RDF/XML format, so I updated my code to convert the Chempedia Substances data into RDF/XML instead of N3 (I have asked Rich to put a new download link online). This is the Groovy code I used:

Oscar uses a Maximum Entropy Markov Model (MEMM) based on n-grams. Peter Corbett has written this up (doi:10.1186/1471-2105-9-S11-S4). So, it basically is statistics once more. If you really want a proper bioinformatics education, so do your PhD at a (proteo)chemometrics department.

The two earlier posts in this series showed screenshots of results of Oscar, but the title also promised results by Lezan’s ChemicalTagger. Sam helped with getting the HTML pages online via the Cambridge Hudson installation. Where Oscar find named entities (chemical compounds, processes, etc), ChemicalTagger finds roles, like solvent, acid, base, catalyst. Roles are properties of chemical compounds in certain situations.

Linus’ law:

Say, you have your own dictionary of chemical compounds. For example, like your company’s list of yet-unpublished internal research codes. Still, you want to index your local listserv to make it easier for your employees to search for particular chemistry you are working on and perhaps related to something done at other company sites. This is what Oscar is for.

One goal of my three month project is to take Oscar4 to the community. We want to get it used more, and we need a larger development community. Oscar4 and the related technologies do a good, sometimes excellent, job, but have to be maintained, just like any other piece of code. To make using it easier, we are developing new APIs, as well as two user-oriented applications: a Taverna 2 plugin , and command line utilities.

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.