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One Registration Number Gives Multiple Structures on ChemSpider. Why?

21 Nov

I was approached today with a question regarding the contents of the ChemSpider database. I have commented previously about the fact that there are quality issues based on some of the depositions but that these are being cleaned up fairly quickly because of the efforts of our curation processes, both robotic and manual. The question was regarding the fact that there were two structures on ChemSpider with the registry number 34090-76-1. This is not uncommon. There are occasions when a registry number is appropriate for a particular salt form while the associated structure is the neutral compound. So, the registry number will be on the database for both the neutral compound and the salt. However, this situation was different…it was down to the position of the double bond. The person was out to confirm the position of that double bond. It was not easy for me to confirm.

What was MORE confusing was what the person had already extracted information from an STN Registry Search. That search provided the following information:

CAS Name: 1,3-Isobenzofurandione, tetrahydro-5-methyl- (CA INDEX NAME)
Other listed names:
Cyclohexene-1,2-dicarboxylic anhydride, 4-methyl- (8CI)
4-Methyltetrahydrophthalic acid anhydride
5-Methyltetrahydroisobenzofuran-1,3-dione

And the following structure:

Compare this structure with the other two off of ChemSpider shown below in the array of three.

Every_single name from STN is listed as a “tetrahydro” compounds so, there needs to be a double bond in the molecule by default. If there isn’t then the compound is a “hexahydro” compound.

Obviously one of the alternative names for the compound was derived from phthalic acid anhydride and this suggests that the “missing double bond” should be at the ring junction as shown.

Included in the STN record is the tag “IDS” tag in the “CI” or “chemical Indexing” field. The term IDS stands for “Incompletely Defined Substance”. So, this is an example of a registry number being allocated to a compound that, in this case, is known to have an additional double bond but it is not shown on the chemical structure displayed in the STN search results but ICS declares it as being “incompletely defined”. Some might say that the fact that ChemSpider has two structures associated with the registration number but each with the double bond in a different position is appropriate. But likely those specific compounds have their OWN registry numbers. So, what should we do?

1) Remove the registry number 34090-76-1 associated with both structures?
2) Leave as is?
3) Add a new term ICS for such records and submit the new incompletely defined substance as a new form of structure?
4) Add NEW registry numbers associated with the individual structures (which someone will need to source since I don’t have them)
5) Something else?

I welcome any or all input. Based on input I will simply login to ChemSpider, make the edit and the information is changed (for addition or removal of identifiers). By working together like this there is an iterative improvement in the quality of structure-name pairs for the benefit of chemists, just as shown with the recent Wikipedia examination of Taxol.

 

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 November 21, 2007 in ChemSpider Chemistry

 

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