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Tuesday, July 31, 2007

Optical Chemical Structure Recognition

Days after the release of OSRA last week, I saw the optical chemistry structure recognition on the front page of my favorite Dutch /. equivalent, Tweakers.net, Duitsers leren computer chemische structuren herkennen, written by René Gerritsen. The article discusses the Fraunhofer Institute's ChemoCR, which was, IIRC, presented as poster at last year's German Conference on Chemoinformatics (to be held again this year). Meanwhile, the CCL.net mailing list had a discussion on the alternatives too; I think it is fair to say that the chemical community realizes the important of these tools. Below is a short overview of the available tools, including some important information regarding integration into workflows.

ChemoCR
ChemoCR seems to be proprietary software, as I could not find any download, and InfoChem seems to be the party to sell licenses. The screenshot in the Tweakers.net article seems to show that is is written in Java, but that hardly matters if not open source. The project is said to have started three years ago.

CLiDE
CLiDE is another commercial (expensive) program to do the job. It was developed more than ten years ago, and the most recent scientific publication is from 1997 (as the webpage states).

OSRA
OSRA (see my previous blog) is opensource and uses the GPL license. It is written in C++. It does not as feature complete as ChemoCR yet, but that will surely come. This project is surely the youngest project.

Kekule
I have not picked up copy of the paper Kekule: OCR-optical chemical (structure) recognition cited by Tony, so cannot say much about that right now.

It is obvious that only OSRA lends itself to embedding in reproducable workflows. Debra Banville reviewed the two commercial programs CLiDE and ChemoCR last year, along with a few other text mining tools in chemoinformatics. I am curious about her opinion of the new opensource tools in this arena.