The presentation I gave is below and loaded on SlideShare in case you want to download it.

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 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!

If you happen to be coming to the ACS and are interested in ChemSpider and how RSC informatics contributes to the world of chemistry please do find time to come and visit the RSC booth and, if you have time, let’s sit over a computer and a coffee and chat!

PAPER ID: 15442 PAPER TITLE: “ChemSpider as a chemical term resolver” (final paper number: 131) DAY & TIME OF PRESENTATION: March 29, 2012 from 10:00 am to 10:20 am LOCATION: San Diego Convention Center , Room: Room 27A

PAPER ID: 10915 PAPER TITLE: “Great promise of navigating the internet using InChIs” (final paper number: 101) DAY & TIME OF PRESENTATION: March 28, 2012 from 9:05 am to 9:35 am LOCATION: San Diego Convention Center , Room: Room 27A

PAPER ID: 10902 PAPER TITLE: “Chemistry made mobile – the expanding world of chemistry in the hand” (final paper number: 68) DAY & TIME OF PRESENTATION: March 26, 2012 from 2:45 pm to 3:20 pm LOCATION: San Diego Convention Center , Room: Room 25C

PAPER ID: 11299 PAPER TITLE: “Social networking tools as public representations of a scientist” (final paper number: 123) DAY & TIME OF PRESENTATION: March 28, 2012 from 2:25 pm to 2:50 pm LOCATION: San Diego Convention Center , Room: Room 25C

PAPER ID: 10893 PAPER TITLE: “Teaching NMR spectroscopy using online resources from the Royal Society of Chemistry” (final paper number: 61) DAY & TIME OF PRESENTATION: March 25, 2012 from 2:50 pm to 3:10 pm LOCATION: Westin San Diego , Room: Diamond II

If any of you are attending ScienceOnline2012 or watching it via Twitter (for example), then you will likely see popping up as @ChemConnector.

If you want to know more about me I am on many of the Social Networks as listed below and actually am very passionate about teaching people about how to get into the Social Network as a scientist. My recent presentation on this is on Slideshare here.

If you are interested in hearing more about the ChemSpider database, a database of >26 million unique chemicals, sourced from over 400 data sources and linking many of these together on the web, then please comment on this post or email me directly at tony27587ATgmailDOTcom and if there is enough interest I will set aside some time to give a couple of demos in one of the rooms at the conference.

This weekend I have spent sometime helping to get some of the ScienceOnline attendees onto the ScientistsDB and they are presently adding/finishing their ScientistsDB pages:

Walter Jessen

Kristi Holmes

Bora Zivkovic

Sarah Chow

Sean Ekins

Myself

If you would like a page on ScientistsDB simply register here and then use this page to learn how to create an article. Ask me for help if you need it.

See you at ScienceOnline2012

The first video is the 60 seconds of stopped motion action ONLY

The second video includes the introduction and conclusion video shots by Mark.

I’ve been watching a number of amusing videos that have been showing up on YouTube of late and, as a bit of an exercise nut, I have posted a couple of funny ones to my Exercise blog [1,2]. Last night, while helping my friend Mark Jensen do some stopped-motion photography while he was painting a sign, I happened upon the process by which these types of movies are made. It’s possible to make them using XtraNormal. Since it is possible to make the first one for free…I had enough credits at least to do what I wanted to do…

So, I made an XtraNormal movie about the situation about “Adult Film Stars and Scientists on Wikipedia”and the development of ScientistsDB. I kind of dedicated the movie to ScienceOnline 2012 as that is where I suggested the fictional discussion between “Sean and Tony” would take place.

I’m sure there are going to be a lot of interesting discussions at ScienceOnline2012 and look forward to seeing everyone there. By the way, if you have been involved with any semantic web projects or projects using Linked Open Data please connect with myself @chemconnector or @kristiholmes on Twitter as we’d like to invite you to give a short (3-4 min) talk at ScienceOnline2012.

PAPER ID: 15442 PAPER TITLE: “ChemSpider as a chemical term resolver”

PAPER ID: 10915 PAPER TITLE: “Great promise of navigating the internet using InChIs”

PAPER ID: 10902 PAPER TITLE: “Chemistry made mobile – the expanding world of chemistry in the hand”

PAPER ID: 11299 PAPER TITLE: “Social networking tools as public representations of a scientist”

PAPER ID: 10893 PAPER TITLE: “Teaching NMR spectroscopy using online resources from the Royal Society of Chemistry”

I’m also listed as a co-author on a number of other presentations and a poster. I’m glad the vacation is over. Time to get back to work, focus the mind and start being productive again! I love the holidays…it’s really a great time to connect with family but just like cardiovascular exercise I lose the ability to think clearly and multitask very quickly. I formally start back to work tomorrow and am already getting the gears rolling again to get myself back up to speed. 2012..here we come.

Join ScientistsDB

Recently I wrote about the issues of notability for scientists versus porn stars. It seemed to kick off quite a discussion…40 comments, 100 Tweets, comments off my blog on other people’s sites. It got mentioned on Wikipedia Signpost..and I take that as a compliment! There are some comments made on various Wikipedia pages [for example, 1]. Not everyone agreed with what I had to say and I received some GOOD guidance and input about how to improve the articles on Wikipedia that I had been writing. There were some supporting comments about how it was appropriate for me to write about people I know (in regards to the Conflict of Interest on Wikipedia).

When I originally wrote the post I was in a particularly “ranting” type of mood based on a few other things going on in regards to other systems, especially in regards to who makes final decisions. In retrospect some of the issues I blogged about had been brought up in various forms by other people over the years and in some ways my comments were “nothing new”. However, it is clear that the exposure the post got did resonate with a number of people.

I have sat with a number of friends and chatted, over a “cool glass of water” (or more), and chatted about exposure for scientists in general. We chatted about Wikipedia articles, about LinkedIn as a networking site for professionals, about the new systems such as ProSkore, and whether Klout would persist as a system for measuring influence.

Sean Ekins and I have introduced two wikis to the community…one for Scientific Mobile Apps and one for Scientific Databases. One addition to the family of scientific wikis that makes sense, based on the recent experiences with Wikipedia and the discussions around notability guidelines for scientists, is the new wiki ScientistsDB.

This wiki is for ANY scientist to have a wiki page about them online. We have no notability guidelines in place, and hopefully will not need them. Time will tell.  The hope is that scientists will contribute their own articles, that the community will also contribute/edit/expand and that ultimately, when the article is in good enough shape, it might be used as the source of an article on Wikipedia. There it can be challenged, discussed, edited and moved through all of the potential phases of a Wikipedia article before it is accepted. We believe that all scientists are entitled to a presence that ScientistsDB can enable. As the data are gathered then we have the possibility of starting to form network maps, relationships and connections that would have been unavailable before. We have a way to introduce scientists working in the same domain, connecting people working on the same classes of compounds, diseases, genes, etc. This is all part of a potential future…for now the Wikipedia articles for scientists (almost 50,000 of them) have been harvested and kept categorized according to Wikipedia categories and all scientists are welcomed to add their own articles. All content is licensed according to CC-BY-SA 3.0.

For now we are starting to get articles. A good model article is from Alex Clark.

We look forward to your thoughts and comments!

Our recent Drug Discovery Today article

One of the highlights of the past year has been my continued collaborations with Sean Ekins on the issues of data quality, modeling of data and the applications of mobile technologies. Recently our commentary on the long term cost of inferior database quality was published in Drug Discovery Today and is available online here.