{ "version": "https://jsonfeed.org/version/1.1", "title": "chem-bla-ics", "description": "Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.", "home_page_url": "https://chem-bla-ics.linkedchemistry.info/", "feed_url": "https://chem-bla-ics.linkedchemistry.info/2007/07/31/optical-chemical-structure-recognition.json", "icon": "https://chem-bla-ics.linkedchemistry.info/assets/images/chem-bla-ics_logo.png", "language": "en", "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286", "_orcid": "0000-0001-7542-0286" } ], "items": [ { "id": "https://doi.org/10.59350/gh6e5-t2g74", "url": "https://chem-bla-ics.linkedchemistry.info/2007/07/31/optical-chemical-structure-recognition.html", "title": "Optical Chemical Structure Recognition", "content_html": "

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

\n\n

ChemoCR

\n

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

\n\n

CLiDE

\n

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

\n\n

OSRA

\n

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

\n\n

Kekule

\n

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

\n\n

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

\n\n

References

\n
\n
Banville, D. L. (2006). Mining chemical structural information from the drug literature. Drug Discovery Today, 11(1–2), 35–42. https://doi.org/10.1016/s1359-6446(05)03682-2 CrossRef Scholia
\n
McDaniel, J. R., & Balmuth, J. R. (1992). Kekule: OCR-optical chemical (structure) recognition. Journal of Chemical Information and Computer Sciences, 32(4), 373–378. https://doi.org/10.1021/ci00008a018 CrossRef Scholia
\n
Simon, A., & Johnson, A. P. (1997). Recent Advances in the CLiDE Project:  Logical Layout Analysis of Chemical Documents. Journal of Chemical Information and Computer Sciences, 37(1), 109–116. https://doi.org/10.1021/ci9601022 CrossRef Scholia
\n
", "summary": "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 importance of these tools. Below is a short overview of the available tools, including some important information regarding integration into workflows.", "date_published": "2007-07-31T00:10:00+00:00", "date_modified": "2025-10-11T00:00:00+00:00", "tags": ["cheminf"], "_references": [ { "url": "https://doi.org/10.1021/ci9601022", "doi": "10.1021/ci9601022" } , { "url": "https://doi.org/10.1021/ci00008a018", "doi": "10.1021/ci00008a018" } , { "url": "https://doi.org/10.1016/S1359-6446(05)03682-2", "doi": "10.1016/S1359-6446(05)03682-2" } ], "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ] } ] }