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Converting Images of Chemical Structures to “Real” Structures

20 Jul

There are many benefits to being on the CHMINF and CCL distribution lists. I recommend them. At the end of today an announcement regarding OSRA dropped into both of them. OSRA – Optical Structure Recognition Application.

It is declared as: “a freely available software is a new addition to the set of chemoinformatics tools available from the Computer-Aided Drug Design Group at the NCI-Frederick. OSRA is a utility designed to convert graphical representations of chemical structures, such as they appear in journal articles, patent documents, textbooks, trade magazines etc., into SMILES. OSRA can read a document in any of the over 90 graphical formats parseable by ImageMagick (GIF, JPEG, PNG, TIFF, PDF, PS etc.) and generate the SMILES representation of the molecular structure images encountered within that document.

A free standalone version of the software can be downloaded from http://cactus.nci.nih.gov/osra/ or tested online at http://cactus.nci.nih.gov/cgi-bin/osra/index.cgi

Rzepa et al have reported previously on “machine vision methods for the identification of chemical composition diagrams from two-dimensional digital raster images.” It’s a good foundation document for understanding some of the challenges with converting structure images to a chemical structure format

Work in this area has gone on for many years with a patent granted for Boyer et al, with the development of CLiDE, Kekule and recently CSR.

I’ve had a lot of interest in these technologies in relation to other work I’ve participate in – the encoding of chemical structures into barcodes (Patent Pending 10/382,461) with the intention of putting chemical databases literally in your hands.

Structure on a PDA

With all these efforts, and based on my exposure to these technologies over the years, my comments are…it’s definitely work worth doing and the efforts have only been partially successful at best (again based on my personal experiences). So, with the announcement of OSRA, and with much excitement I started hitting the online system with challenges.

My observations to date applied to exports of 300dpi TIFFs from Chemsketch
1) Hexylbenzene converted perfectly..as did many other simple structures…simple chains and rings.
2) Bridgehead compounds are problematic…crossed bonds are the issue it appears
3) Stereobonds cause problems…maybe at conversion…maybe with SMILES handling (to be investigated!) Less than 50% success at retaining appropriate stereobonds…while quick visual inspection suggested structures were the same only alignment of the molecules and careful examination showed that in a number of cases they were not matching. The easiest was to compare was comparison of systematic names or InChI.
4) Organometallics were problematic…an example shown below. The pair of structures on the left were derived from the conversion of the structure on the right. Notice the Al was converted to Ar (aryl?), a bond was severed, an oxygen atom was lost.

al_converted.png

OSRA is clearly a work in progress…but a valid and worthy effort I will support with great enthusiasm. From the point of view of ChemSpider I imagine a time when OSRA is ripping it’s way through PDF files and converting structures on the fly, with a very low error rate and extracting those structures from Open Access chemistry articles to populate ChemSpider and make those Open Access Articles searchable by both structure/substructure and of course by text through the ChemRefer search engine.

That being said…what makes all of this easier is for Adobe to collaborate with the chemistry community and embed InChI tags or even connection tables into the PDF format. A number of years ago ACD/ChemSketch was extended to allow the export of PDF format reports with the structure connection tables tagged in the PDF format. All ChemSketch PDF generated files are therefore structure searchable. Anybody out there have connections into Adobe Life Sciences?

ACD/Labs have just done the same for PNG files by embedding the InChI codes directly into the PNG format when exported from ACD/ChemSketch. This was at the request of the Wikipedia community.

So…my commendations to Marc Nicklaus and Igor Filippov at the Computer-Aided Drug Design Group at the NCI-Frederick. OSRA release 1 looks like it is heading in the right direction but has some hills to climb yet. SIgn me up to help.

 

About tony

Antony (Tony) J. Williams received his BSc in 1985 from the University of Liverpool (UK) and PhD in 1988 from the University of London (UK). His PhD research interests were in studying the effects of high pressure on molecular motions within lubricant related systems using Nuclear Magnetic Resonance. He moved to Ottawa, Canada to work for the National Research Council performing fundamental research on the electron paramagnetic resonance of radicals trapped in single crystals. Following his postdoctoral position he became the NMR Facility Manager for Ottawa University. Tony joined the Eastman Kodak Company in Rochester, New York as their NMR Technology Leader. He led the laboratory to develop quality control across multiple spectroscopy labs and helped establish walk-up laboratories providing NMR, LC-MS and other forms of spectroscopy to hundreds of chemists across multiple sites. This included the delivery of spectroscopic data to the desktop, automated processing and his initial interests in computer-assisted structure elucidation (CASE) systems. He also worked with a team to develop the worlds’ first web-based LIMS system, WIMS, capable of allowing chemical structure searching and spectral display. With his developing cheminformatic skills and passion for data management he left corporate America to join a small start-up company working out of Toronto, Canada. He joined ACD/Labs as their NMR Product Manager and various roles, including Chief Science Officer, during his 10 years with the company. His responsibilities included managing over 50 products at one time prior to developing a product management team, managing sales, marketing, technical support and technical services. ACD/Labs was one of Canada’s Fast 50 Tech Companies, and Forbes Fast 500 companies in 2001. His primary passions during his tenure with ACD/Labs was the continued adoption of web-based technologies and developing automated structure verification and elucidation platforms. While at ACD/Labs he suggested the possibility of developing a public resource for chemists attempting to integrate internet available chemical data. He finally pursued this vision with some close friends as a hobby project in the evenings and the result was the ChemSpider database (www.chemspider.com). Even while running out of a basement on hand built servers the website developed a large community following that eventually culminated in the acquisition of the website by the Royal Society of Chemistry (RSC) based in Cambridge, United Kingdom. Tony joined the organization, together with some of the other ChemSpider team, and became their Vice President of Strategic Development. At RSC he continued to develop cheminformatics tools, specifically ChemSpider, and was the technical lead for the chemistry aspects of the Open PHACTS project (http://www.openphacts.org), a project focused on the delivery of open data, open source and open systems to support the pharmaceutical sciences. He was also the technical lead for the UK National Chemical Database Service (http://cds.rsc.org/) and the RSC lead for the PharmaSea project (http://www.pharma-sea.eu/) attempting to identify novel natural products from the ocean. He left RSC in 2015 to become a Computational Chemist in the National Center of Computational Toxicology at the Environmental Protection Agency where he is bringing his skills to bear working with a team on the delivery of a new software architecture for the management and delivery of data, algorithms and visualization tools. The “Chemistry Dashboard” was released on April 1st, no fooling, at https://comptox.epa.gov, and provides access to over 700,000 chemicals, experimental and predicted properties and a developing link network to support the environmental sciences. Tony remains passionate about computer-assisted structure elucidation and verification approaches and continues to publish in this area. He is also passionate about teaching scientists to benefit from the developing array of social networking tools for scientists and is known as the ChemConnector on the networks. Over the years he has had adjunct roles at a number of institutions and presently enjoys working with scientists at both UNC Chapel Hill and NC State University. He is widely published with over 200 papers and book chapters and was the recipient of the Jim Gray Award for eScience in 2012. In 2016 he was awarded the North Carolina ACS Distinguished Speaker Award.
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Posted by on July 20, 2007 in Uncategorized

 

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