Scholar Alert: New citations to my articles

The Chemical Ecology of Soil Organic Matter Molecular Constituents

MJ Simpson… – Journal of Chemical Ecology, 2012

Abstract Soil organic matter (OM) contains vast stores of carbon, and directly supports
microbial, plant, and animal life by retaining essential nutrients and water in the soil. Soil OM
plays important roles in biological, chemical, and physical processes within the soil, and …

Bioinformatics and variability in drug response: a protein structural perspective

JL Lahti, GW Tang, E Capriotti, T Liu… – Journal of The Royal Society …, 2012

Abstract Marketed drugs frequently perform worse in clinical practice than in the clinical trials on which their approval is based. Many therapeutic compounds are ineffective for a large subpopulation of patients to whom they are prescribed; worse, a significant fraction of …

From theory of spectra to standardless analysis of molecular objects

LA Gribov… – Journal of Analytical Chemistry, 2012

Abstract The authors discuss the methodology of quantitative analysis of pure substances
and mixtures by optical spectra (IR, Raman, UV, etc.) without using samples of standard
composition (standardless molecular spectral analysis). An algorithm of quantitative …

Aligning chemical structure diagrams with local search

M Hilbig… – Journal of Cheminformatics, 2012

Chemists working in biomolecular application projects are usually looking at many related
molecules (eg results of a virtual screening run, lead series development or library design).
For a convenient visual analysis of this data it is essential that differences between …

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One of the parts of the conversation was regarding the work put in to clean up chemistry data on Wikipedia. What seems like an eternity ago I did “Dedicate Christmas Time to the Cause of Curating Chemistry on Wikipedia” and initiated a project to check every chemical compound on Wikipedia, bond by bond, atom by atom. However, I very quickly connected with Walkerma who then introduced me to a number of other Wikipedia Chemistry people. I started participating in IRC Chats with this group and we started exchanging comments about how we could move the project along. It was a pleasure to work with the team and while I did continue to participate it was nowhere near the level that I had contributed in the early days of the project. The project was a collaborative effort for sure, one of the best I have been involved with over the past few years.

When the original article on Nature.Com was published it stated “In fact, notes Williams, Wikipedia proved the most reliable source of structure information in that experiment – largely because he had led an effort to clean up the site’s 13,000 structures.” I definitely didn’t want that statement in the article and had specifically requested that I was represented as being part of a collaborative effort. I did not lead the project…I was a part of it only. So, with a couple of email exchanges with the author of the article, Richard van Noorden, the language was changed to “In fact, notes Williams, Wikipedia proved the most reliable online source of structure information in that experiment – largely because of an effort to clean up the site’s 13,000 pages about drugs and chemicals”. It’s a subtle edit but I definitely did not want to carry the responsibility for leading a project that was an ideal representation of crowdsourcing, collaboration and caring for chemistry on Wikipedia. And, to clarify…I know for a fact that all pages are not fully curated and validated yet…it’s a long process!!!

ChemSpider as a chemical term resolver

In recent years, in parallel with the general broad trend of information proliferation, many tens of public chemical databases have been created and made available using internet technologies. In many cases fluent data exchange has occurred between these various databases as they source information from one another. While this has the advantages of linking together multiple data sources the results also include the proliferation of errors across the various databases. The lack of a public authority to resolve such errors significantly affects the quality of freely accessible chemical information. While ChemSpider has previously allowed a crowdsourcing approach to curation efforts have now migrated to addressing this problem using a “federated resolver” approach. This presentation will report on our work in this area.

On the Accuracy of Chemical Structures Found on the Internet

The Internet has been widely lauded as a great equalizer of information access.  However, the absence of any central authority on content places the burden on the end-user to verify the quality of the information accessed.  We have examined the accuracy of the chemical structures of ca. 200 major pharmaceutical products that can be found on the internet.  We have demonstrated that while erroneous structures are commonplace, it is possible to determine the correct structures by utilizing a carefully defined structure validation workflow.  In addition, we and others have shown that the use of un-curated structures affects the accuracy of cheminformatics investigations such as QSAR modeling. Furthermore, models built for carefully curated datasets can be used to correct erroneously reported biological data.  We posit that chemical datasets must be carefully curated prior to any cheminformatics investigations.  We summarize best practices developed in our groups for data curation.

Social networking tools as public representations of a scientist

The web has revolutionized the manner by which we can represent ourselves online by providing us the ability to exposure our data, experiences and skills online via blogs, wikis and other crowdsourcing venues. As a result it is possible to contribute to the community while developing a social profile as a scientist. At present many scientists are still measured by their contributions using the classical method of citation statistics and a number of freely available online tools are now available for scientists to manage their profile. This presentation will provide an overview of tools including Google Scholar Citations and Microsoft Academic Search and will discuss how these are and other tools, when integrated with the ORCID identifier, may more fully recognize the collective contributions to science. I will also discuss how an increasingly public view of us as scientists online will likely contribute to our reputation above and beyond citations.

The great promise of navigating the internet using InChIs

The InChI, the International Chemical Identifier, has been the basis of both indexing and deduplication of the ChemSpider database since the inception of the platform. When the InChI was adopted we envisaged a future whereby the identifier would proliferate across journals, databases and the internet in general providing us a basis for “structure searching the internet”. This presentation will provide an overview of how the InChI has facilitated the integration of ChemSpider to chemistry on the internet, some of the surprising findings that have resulted from this work and extrapolate the influence of InChIs into the future for a chemically enabled web.

The Royal Society of Chemistry hosts an online resource, ChemSpider, as a structure centric database for chemists linking over 25 million chemicals to 400 internet sites. As a crowdsourced environment members of the chemistry community can deposit spectral data to the database. Almost 2000 NMR spectra have been submitted to the database and these are the basis of both a gaming environment for learning NMR spectroscopy, the SpectralGame, as well as a new teaching environment known as SpectraSchool. This presentation will provide an overview of these two online resources and how they may be utilized for the purpose of teaching NMR spectroscopy in an Undergraduate Curriculum.

The acknowledgments slide includes:

Alexey Pshenichnov, University of Leicester and Richard Oakley – SpectraSchool

Aileen Day and Martin Walker – Learn Chemistry Wiki

Jean-Claude Bradley, Andrew Lang and Robert Lancashire, ChemDoodle – SpectralGame

Gary Allred and Chi Wang – Synthonix Data

Ryan Sasaki, Sergey Golotvin, Pranas Japertas (ACD/Labs) –Bulk data processing and Spectral Display Widget

Depositors of data – there are many!

We thank all of these individuals and their companies for supporting our efforts!

I will post the presentation to my slideshare account later today and then embed it to the blog also…but, if youa re in San Diego come and hear the talk…

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

In the Triangle we have lots of people involved in cheminformatics and what I would call “advanced data handling” associated with chemistry. We have the universities in the area (Duke, University of North Carolina, North Carolina State University, etc.), we have many companies using cheminformatics (GSK, BASF, Metabolon, to name just three) and government labs such as the EPA and NIEHS dealing with some of the complexities of managing chemistry related data. So, why not bring us together and share experiences, best practices and, even, data! We are also not so far from the government labs in Washington where there are enormous investments in cheminformatics and bioinformatics and we could invite in guest speakers to come and tell us about some of the work they are doing.

Of course, there is no point in throwing a party if no one would show up so this initial blog post is to see whether there is interest in attending a cheminformatics discussion group. The logistics of when, where it would be hosted, how long etc. will be defined once interest is defined.

Because community grows from participation please DO comment on this blog as to whether you would be interested in showing up. The more people that indicate interest the greater the chance that more people would choose to participate. So, simply add a comment, with your name and institutional name, that you would be interested in attending. Also, please pass on the link to this blog post to others and lets see if we can organize ourselves into a community of participation!

The chemical structure of Olympicene

Last year one of the editorial board for ChemSpider SyntheticPages (CSSP), Professor Peter Scott from the University of Warwick, started a discussion with colleagues at the university regarding how to synthesise the compound. The intention was to publish all steps in the synthesis to the CSSP platform. With “the Games” just around the corner, how has the little marathon synthesis progressed so far? How close is the group to completing their work? If you check out the steps on CSSP, one by one, you will see the progress…all syntheses are reported by Anish Mistry from the Fox Group at Warwick University.

Step 1 of the Synthesis of Olympicene on ChemSpider SyntheticPages

Step 2: Hydrogenation of Ethyl 3-(1-pyrenyl)acrylate

Step 3: Hydrolysis of Ethyl 3-(1-pyrenyl)propanoate

Step 4: Chlorination of a carboxylic acid

Step 5: Friedel Crafts cylisation of 3-(1-Pyrenyl)propanoyl chloride

Step 6 of the Synthesis of Olympicene on ChemSPider SyntheticPages

If you check out Step 6 you will see just how close the group is to completing the synthesis. Then it will be on to the analytical work. We are looking forward to hosting the results of the analytical work on the ChemSpider page. Watch this space!