Archive for category ChemSpider Chemistry

Engaging students in publishing on the internet early in their careers

Presentation given at ACS New Orleans Spring Meeting

As a result of the advent of internet technologies supporting participation on the internet via blogs, wikis and other social networking approaches, chemists now have an opportunity to contribute to the growing chemistry content on the web. As scientists an important skill to develop is the ability to succinctly report in a published format the details of scientific experimentation. The Royal Society of Chemistry provides a number of online systems to share chemistry data, the most well known of these being the ChemSpider database. In parallel the ChemSpider SyntheticPages (CSSP) platform is an online publishing platform for scientists, and especially students, to publish the details of chemical syntheses that they have performed. Using the rich capabilities of internet platforms, including the ability to display interactive spectral data and movies, CSSP is an ideal environment for students to publish their work, especially syntheses that might not support mainstream publication.

 

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ChemSpider – disseminating data and enabling an abundance of chemistry platforms

Presentation given at ACS New Orleans Spring Meeting

ChemSpider is one of the chemistry community’s primary public compound databases. Containing tens of millions of chemical compounds and its associated data ChemSpider serves data to many tens of websites and software applications at this point. This presentation will provide an overview of the expanding reach of the ChemSpider platform and the nature of solutions that it helps to enable. We will also discuss some of the future directions for the project that are envisaged and how we intend to continue expanding the impact for the platform.

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Challenging cajoling and rewarding the community for their contributions to online chemistry

Presentation given at ACS New Orleans Spring Meeting

Chemistry online is represented in various ways including publications, presentations, blog posts, wiki-contributions, data depositions, curations and annotations. Encouraging participation from the community to participate in and comment on the information delivered via these various formats would likely provide for a rich dialog exchange in some cases and improved data quality in others. At the Royal Society of Chemistry we have a number of platforms that are amenable to contribution. This presentation will provide an overview of our experiences in engaging the community to interact with our various forms of content and discuss new approaches we are utilizing to encourage crowdsourced participation.

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A Hairy Christmas Story for the Holiday Season

As a scientist myself, and after years of pulling my hair out over various projects (as well as some of the conversations I have with my twin boys) there are times I wish that I wasn’t “thinning on top”. This video uses the holiday season to help encourage those of us who are “follicly challenged” to realize that science will give us the solution. This movie is a collaboration between my good friend Professor Alex Tropsha from the University of North Carolina in Chapel Hill (http://pharmacy.unc.edu/Directory/tropsha) and myself (Antony Williams, http://www.chemconnector.com/) where we did a few takes …literally 8 different shots only, in less than an hour. With a little bit of waxing lyrical to an old classical Christmas Song, and a quick self-training course in Microsoft Movie Maker (BRILLIANT SOFTWARE) I threw this together in about 2 hours. Enjoy! And there is hope for all us who, because of the excess heat from our skulls from “all that thinking”, are evaporating the follicles.

Please do note that Alex is modeling a ChemSpider SyntheticPages labcoat. Want to win one? Then you need to write a few articles here: http://cssp.chemspider.com/

I would like to acknowledge my mother for giving me a singing voice that sounds like I am gargling broken glass.

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Mining public domain data as a basis for drug repurposing #ACSPhilly

Second talk delivered today at ACS Philadelphia…

Mining public domain data as a basis for drug repurposing

Online databases containing high throughput screening and other property data continue to proliferate in number. Many pharmaceutical chemists will have used databases such as PubChem, ChemSpider, DrugBank, BindingDB and many others. This work will report on the potential value of these databases for providing data to be used to repurpose drugs using cheminformatics-based approaches (e.g. docking, ligand-based machine learning methods). This work will also discuss the potentially related applications of the Open PHACTS project, a European Union Innovative Medicines Initiative project, that is utilizing semantic web based approaches to integrate large scale chemical and biological data in new ways. We will report on how compound and data quality should be taken into account when utilizing data from online databases and how their careful curation can provide high quality data that can be used to underpin the delivery of molecular models that can in turn identify new uses for old drugs.

 

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Putting chemistry into the hands of students #ACSPhilly

I had the privilege of co-chairing a session on Mobile Chemistry today with Harry Pence. The session was “Mobile devices, augmented reality, and the mobile classroom”

Putting chemistry into the hands of students – chemistry made mobile using resources from the Royal Society of Chemistry

The increasing prevalence of mobile devices offers the opportunity to provide chemistry students with easy access to a multitude of resources. As a publisher the RSC provides a myriad of content to chemists including an online database of over 26 million chemical compounds, tools for learning spectroscopy and access to scientific literature and other educational materials. This presentation will provide an overview of our efforts to make RSC content more mobile, and therefore increasingly available to chemists. In particular it will discuss our efforts to provide access to chemistry related data of high value to students in the laboratory.  It will include an overview of spectroscopy tools for the review and analysis of various forms of spectroscopy data.

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Introducing the ChemSpider Validation and Standardization Platform

Chemistry is complex. Anybody who has been involved with the creation of electronic datafiles containing thousands of chemical compounds and associated data (chemical names, properties etc) will tell you that errors creep in. ChemSpider has >28 million unique chemical entities and these have been sourced from many different places/groups/individuals. Some of these have been deprecated as we have determined, both manually and algorithmically, that the data are in error. Over the years we have learned a lot about data quality and ways in which algorithms can be applied to data prior to deposition on ChemSpider.

Some obvious structure-based errors that can be checked for would include: hypervalency (e.g. pentavalent carbons), charge imbalance (a compound has no neutralizing counterion for example), absence of stereochemistry (e.g. a compound with 12 possible stereocenters only has one assigned). There are many other such errors that can be detected algorithmically. It’s the old adage of why apply a human to what a computer can fix. With this in mind we have been working on a system called the ChemSpider Validation and Standardization Platform (CVSP for short). This system will serve multiple purposes. It will be one of the foundation blocks for checking structure-based data for our publications (i.e. catch bad chemistry before it is published!), it will be used for validating chemistry for our databases (Natural Product UpdatesMethods in Organic Synthesis and Catalysts and Catalyzed Reactions), it will be used to check and validate depositions going into ChemSpider, it will serve data related to the Open PHACTS project  and it will serve the community by providing an online website where you can upload your own SDF files (and other file formats in future) to validate the structures.

I won’t go into detail here about all of the functionality and capability of the system as we will discuss this in further detail on this blog. However, we will be unveiling the system in its present form at the ACS meeting in Philadelphia. Come along and meet some of the team involved in building CVSP and give us your feedback!

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Presenting on Teaching NMR spectroscopy using online resources from RSC Later Today

I will be presenting on “Teaching NMR spectroscopy using online resources from the Royal Society of Chemistry” later this afternoon at the ACS meeting here in San Diego. I have just finished the acknowledgment slide and it is always fun to see just how collaborative some of our ventures are. In order to provide community resources such as ChemSpider (and its integrated projects such as the Learn Chemistry Wiki and SpectralGame) we depend on willing, creative and collaborative minds. And we work with some of the best!

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, ChemDoodleSpectralGame

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

 

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Presentation at NFAIS 2012 on Five Years of Experience of Crowdsourcing Chemistry for the Community

I just gave a presentation at the NFAIS conference in Philadelphia with the conference focus being “Born of Disruption: An Emerging New Normal for the Information Landscape”. I was on a panel with Lee Dirks from Microsoft Research and Kristen Fisher-Ratan from PLoS. Both gave very interesting talks and it was a pleasure to be on the panel with them.

My talk was entited “Crowdsourcing Chemistry for the Community – 5 Years of Experiences” with the abstract below.

“ChemSpider is one of the internet’s primary resources for chemists. ChemSpider is a structure-centric platform and hosts over 26 million unique chemical entities sourced from over 400 different data sources and delivers information including commercial availability, associated publications, patents, analytical data, experimental and predicted properties. ChemSpider serves a rather unique role to the community in that any chemist has the ability to deposit, curate and annotate data. In this manner they can contribute their skills, and data, to any chemist using the system. A number of parallel projects have been developed from the initial platform including ChemSpider SyntheticPages, a community generated database of reaction syntheses, and the Learn Chemistry wiki, an educational wiki for secondary school students.

This presentation will provide an overview of the project in terms of our success in engaging scientists to contribute to crowdsouring chemistry. We will also discuss some of our plans to encourage future participation and engagement in this and related projects.”

The talk is embedded below. I thank the organizers for the ability to ask questions during the talk and get responses using a clicker feedback system (I didn’t realise ahead of time that the questions would consume a few seconds and ran over on my talk..agh). I will get the answers to the questions and post them in a separate post. Interesting answers…

 

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Improving Online Chemistry One Structure at a Time

Last week I was in the United Kingdom for numerous meetings and at the end of the week struggled to drive north to Macclesfield to the AstraZeneca site there to give a presentation on ChemSpider for an old colleague of mine from the Eastman Kodak company. I had not seen Tony Bristow in well over a decade but we reminisced about the good old days at Kodak (Tony worked in Harrow, UK and I worked in Rochester, NY. Tony is a Mass Spectrometrist and I am an NMR Spectroscopist by training). We also discussed how scientists are increasingly tapping into the ChemSpider resource to aid in the identification of chemical compounds using, especially, Mass Spectrometry. We have numerous examples now of when people are solving their structure ID issues directly by searching ChemSpider and are building up a portfolio of success stories.

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

 

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