The Selected Organic Reactions (SOR) Database: capturing “Lost Chemistry”

Dick Wife, SORD B.V. The Netherlands (www.sord.nl; dick.wife@sord.nl)

A new database is capturing the 80% of Lost Chemistry from theses and dissertations which doesn’t make it into publications and chemists who contribute their data get access to the entire database for free.

SORD, an independent Dutch company, is carefully selecting the synthetic chemistry focused on Life Science research and making this chemistry available in their Selected Organic Reactions (SOR) Database. For the theses/dissertations which they select, SORD excerpts all of the reactions in the Experimental section are excerpted. This means there will still be a small overlap of data with full publications. There will also be a larger overlap with publications such as Notes, Letters or Communications but these do not contain the experimental details. The SOR Database brings all this chemistry to the desktop, every last detail written by the author.

Some time back, SORD looked at around 300k interesting drug-like compounds in the literature and which countries they had come from, and the native language. The English-speaking countries accounted for only 37% of the total. German/Swiss dissertations are often written in English but this is new. The theses and dissertations in the other languages represent more than half of the total. SORD routinely translates German and French experimental texts into English. They are about to start on Chinese and Japanese translations and, if anyone can give them access to Russian theses, they will translate these as well!

A thesis or dissertation is the result of several years of hard work by a research student under the constant supervision of the research leader whose reputation is at stake if the work described is wrong or inaccurate. It is also examined by a committee who decide on awarding the degree, or not. They scrutinize closely the Results & Discussion as well as the Experimental sections. The chemistry is reliable.

Advanced Chemistry Development, Inc (ACD/Labs) is partnering SORD in developing this Database. The SOR Database is available for in-house use with ChemFolder Enterprise or on the Internet with ACD/Web Librarian™. This is a screen-shot of a typical SOR Database record in Web Librarian.

The Reaction Scheme shows every atom (there are no abbreviations). The Experimental  text is edited to ASCII format and the key parameters (Reagent(s), Solvent(s), yield(s), MP(s) and Optical Rotation(s) are displayed in separate Fields, as are the full bibliographic data, making data-mining possible. There is also a link which enables the user to bring up the PDF of each reaction containing all of the spectral and other physical data which SORD does not excerpt. The PDF-EX link is a powerful and unique feature of the SOR Database.

Now some explanation about SORD’s excerption rules. What they call the Reaction Scheme (A + B à C, etc.) contains only the reacting and product compound structures. A Reagent is an essential reaction component of which no part ends up in the product – if it does, it becomes a Reactant! When several reactions are performed before the product is isolated (and characterized) the Reagents and Solvents are listed in Steps. Failed reactions are not excerpted but reactions with poor yields are.

The SOR Database currently contains 170k reactions; the target is one million at the end of 2013. Even this number is a lot smaller than what you find today in the major commercial reaction databases. Back in the nineties, SORD researchers looked at one such large commercial database which then contained 9 million compounds. Sifting through the content for drug-like compounds resulted in just 450k or 5% of the records[1]. Size is one database metric; quality is much more important! In the SOR Database, you will only find characterized products – and no polymers, or compounds with no molecular structure.

Users of the SOR Database also have access to the separate databases which contain the Reagents (ca. 3,000) and Solvents (ca. 450) which have been encountered so far. Often a Reagent is a catalyst (organic/organometallic) but they can also be simple entities like bases, acids, ammonium salts, etc. or complex chiral ligands. Authors give Reagents many different names and so each Reagent (and Solvent) in the SOR Database has been assigned a unique name. This enables rapid searches using the assigned names, again a novel feature of the database. Such searches can bring you to really nice chemistry.

As an Example, the second generation Grubbs olefin metathesis catalyst has been given the name Grubbs 2 catalyst. In the current SOR Database, there are more than 500 reactions where it has been used. Some of these are straightforward; some are not and generate novel ring systems like this one from the Martin group at North Carolina at Chapel Hill:

Searches in the Reactions Scheme, or using Reagent/Solvent names and hit refinement brings you to new chemistry which until now was only found on a dusty shelf in a library. The “Lost Chemistry” is now getting smaller as SORD carefully selects and excerpts the reactions which deserve a new life. The SOR Database is essential for novelty searches and it is a powerful supplement for the other commercial reaction databases.

Finally some more good news for academic research chemists; your data will be readily accessible to the whole chemical world who will cite your work in their publications. The chemistry which you never published may be just what others are looking for. Routinely SORD excerpts the complete collection of theses and dissertations from research supervisors; they will be more than happy to see your work appear in the next SOR Database!

“ChemSpider Mobile is a free iOS app (iPhone, iPod, iPad) for searching the ChemSpider online chemical database. It provides the ability to search by drawing a chemical structure, or entering a compound name. The app is very straightforward and easy to learn. Search results are shown in a list showing structure and names. Any search result can be examined in more detail by launching the mobile browser and viewing the structure on the ChemSpider web page. Although the ChemSpider web page is designed to work well on mobile browsers, the mobile app is more convenient to use, and is currently the best way to search by structure from a mobile device. The structure drawing capabilities are provided by the embedded version of the Mobile Molecular DataSheet. The app was built by Molecular Materials Informatics, on behalf of the Royal Society of Chemistry.”

We will look at developing an Android app for ChemSpider, taking into account what we learn from the early use of the iOS Mobile app.

A screencast of the functionality of ChemSpider Mobile is available below.

Please drop by and say “Hi!”

We’d like to repeat our invitation to everyone at the conference to drop by the RSC booth (Booth 1100). Where, of course you can chat with the ChemSpider team, get a quick demo (and find out more about our latest features), pick up our hot-off-the-press User Guide or scoop some exclusive ChemSpider goodies!

To celebrate the release of the new iPhone/iPad app* we have a limited number of covers for 3G and 4G iPhones as well as iPads

*The app itself is free to download from the AppStore.

You can also find out about lots of other things that the RSC does: from publishing books and journals to the promotion of chemistry worldwide. We’ll also have lots of information on our new e-membership option, which is making its’ debut at this meeting. Also keep an eye out for members of our Editorial staff from journals including: OBC, MedChemComm, PCCP, Soft Matter and RSC Advances, who will be scouring the conference in search of lots of new and exciting research.

Natural Product & Synthetic Chemists

I’d like to make an extra special invitation to any Synthetic chemists and Natural products chemists – from PhD students to Professors (please pass this on to all your friends and colleagues who will be at the meeting). The ChemSpider team really wants to hear about your research. Tell us about your latest publication or the work that you are most proud of, and we can make sure that your key compounds from these publications are in ChemSpider, on a platform freely accessible to chemists everywhere. If you are more interested in methodology you shouldn’t feel left out – ask us about ChemSpider Synthetic Pages.

ChemSpider related talks and workshops

Antony Williams (most-definitely the hardest working man I know) is giving a number of talks and workshops (details below) which are sure to be entertaining as well as thought-provoking and will be well-worth squeezing into your schedule.

We look forward to meeting you.

“Aligning scientific expertise and passion through a career path in the chemical sciences”

Colorado Convention Center, Room: 110, Sunday 28^th August 2011, 1.40PM – 2PM

“Chemistry in the hand: The delivery of structure databases and spectroscopy gaming on mobile devices”

Colorado Convention Center, Room: 110, Monday 29^th August 2011, 9.05AM – 9.35AM

“ChemSpider: Does community engagement work to build a quality online resource for chemists?”

Colorado Convention Center, Room: 110, Tuesday 30^th August, 10.10AM – 10.50AM

“An Introduction to ChemSpider – A Combination Platform of Free Chemistry Database, Free Prediction Engines and Wiki Environment”

Colorado Convention Center, Room 503, Wednesday 31^th August 2011, 08.30AM – 11AM

“Structure representations in public chemistry databases: The challenges of validating the chemical structures for 200 top-selling drugs”

Colorado Convention Center, Room: 110, Wednesday 31^st August 2011, 10.45AM – 11.05AM

“ChemSpider Mobile is a free iOS app (iPhone, iPod, iPad) for searching the ChemSpider online chemical database. It provides the ability to search by drawing a chemical structure, or entering a compound name. The app is very straightforward and easy to learn. Search results are shown in a list showing structure and names. Any search result can be examined in more detail by launching the mobile browser and viewing the structure on the ChemSpider web page.

Although the ChemSpider web page is designed to work well on mobile browsers, the mobile app is more convenient to use, and is currently the best way to search by structure from a mobile device. The structure drawing capabilities are provided by the embedded version of the Mobile Molecular DataSheet. The app was built by Molecular Materials Informatics, on behalf of the Royal Society of Chemistry.”

An early view screencast of the functionality of ChemSpider Mobile is now available.  New movies showing the details of the app will follow in the near future but this is an early view for interested parties.

Antony Williams, Vice President of Strategic Development for ChemSpider comments “Elemental offers ease of deployment and flexibility in structure drawing to our community of users and we are happy to embrace this web-based structure drawing platform as an entry point to the rich resources of ChemSpider.”

Dr Mike Hartshorn, Director and CSO of Dotmatics, said “We are delighted to be working with such a well-known chemistry resource as ChemSpider. The new tools will allow simple access to the wide range of structures and related information that is maintained by ChemSpider and the RSC”.

About Dotmatics
Dotmatics Limited (www.dotmatics.com) is a leading provider of web-based database integration and visualisation tools for use within the life sciences industry.

About the Royal Society of Chemistry
The Royal Society of Chemistry is the UK Professional Body for chemical scientists and an international Learned Society for the chemical sciences with more than 47,500 members worldwide. It is a major international publisher of chemical information, supports the teaching of chemical sciences at all levels and is a leader in bringing science to the public. www.rsc.org

About ChemSpider
ChemSpider offers a structure-centric community for chemists to resource data.  Offering access to over 25 million unique chemical entities from over 400 data sources and by providing a platform for crowd-sourced deposition, annotation, and curation, it is the richest source of free integrated chemistry information available online.  ChemSpider delivers data and services to enable the semantic web for chemistry.  www.chemspider.com

Contacts:
Mike Hartshorn
Dotmatics Limited, The Old Monastery
Windhill, Bishops Stortford
CM23 2ND, UK
Tel: +44 1279 654123
Email: info@dotmatics.com
www.dotmatics.com

Antony Williams
ChemSpider, Royal Society of Chemistry
904 Tamaras Circle
Wake Forest, NC 27587
Tel: 919-201-1516
Email: info@chemspider.com
www.chemspider.com

ChemSpider – Is This The Future of Linked Chemistry on the Internet?
ChemSpider was developed with the intention of aggregating and indexing available sources of chemical structures and their associated information into a single searchable repository and making it available to everybody, at no charge. There are now hundreds of chemical structure databases such as literature data, chemical vendor catalogs, molecular properties, environmental data, toxicity data, analytical data etc. and no single way to search across them. Despite the diversity of databases available online their inherent quality, accuracy and completeness is lacking in many regards. ChemSpider was established to provide a platform whereby the chemistry community could contribute to cleaning up the data, improving the quality of data online and expanding the information available to include data such as reaction syntheses, analytical data and experimental properties. ChemSpider has now grown into a database of almost 25 million chemical substances, grows daily, and is integrated with over 400 sources, many of these directly supporting the Life Sciences. This presentation will provide an overview of our efforts to improve the quality of data online, to provide a foundation for a linked web for chemistry and to provide access to a set online tools and services to support access to these data.

http://www.chemspider.com/Sitemap.aspx is the new sitemap for ChemSpider which lists all of the different pages in it and will help you to get an overview of all the different things that you can see and do on ChemSpider.

There are also brief descriptions about each page which will, where necessary, suggest input examples if you just want to try something out but aren’t quite sure what to type into the boxes. If you are a ChemSpider depositor or curator and view the sitemap when logged in you will see additional pages relevant to your assigned roles.

We are also working on providing access to ChemSpider SyntheticPages in the same way and the first screen shot is shown at the bottom. Things are always changing and, I believe, for the better.