ChemSpider Blog

We are presently receiving sign ups for our training session on ChemSpider. The session will be on Monday afternoon between 4-6pm (details below) It is free to attend and we’d love to see you there if you are in San Francisco at that time. Sign up here…

Royal Society of Chemistry
How to get started with ChemSpider – Searching, Structure Deposition and Database Curation
Instructor(s): Antony Williams, VP Strategic Development ChemSpider
Where: Moscone Center
Room: 110
When: Monday, March 22, 4:00 PM – 6:00 PM
>> Click here to register for this workshop
This session will give the opportunity to learn more about how to search ChemSpider, how to deposit your structures and how you can participate in curation of the data.  Presenter: Antony Williams, VP Strategic Development ChemSpider

For those of you looking for some assistance on either searching ChemSpider or how to become more involved in the community by depositing your own structures or adding links to your research there is now some updated documentation available under the support page of ChemSpider.

There is a Guide to Database Curation and Structure Deposition and four Quick Cards to help with chemical name searching, structure searching, single structure deposition and adding links to the record view.

Over the past three years we have received a lot of kudos from the users of ChemSpider, mostly via email. I’d now like to make a direct and some would say quite cheeky request for community participation. It will result in us immortalizing your participation on the pages of ChemSpider. We’d like to gather together some comments/quotes/statements from the community about how valuable ChemSpider has become for you and how you might be using it. We’d like to use these quotes as some sort of rolling banner (as yet to be designed!) as well as maybe in some presentations etc.

We’d appreciate your comments about ChemSpider and encourage you to comment on this blog if you would. Please leave your name and, if appropriate and should you wish, your organization name. We understand that we live in times where it is necessary to have the disclaimer “these views represent the view of the individual and not XXXX organization” so feel free to just sign yourself “a medicinal chemist” or “a Happy ChemSpider User” . We don’t ask for much in exchange for the work we’ve been doing for the past few years and yes, I agree it is cheeky, but as my son reminds me regularly …if I don’t ask I don’t get

Of, feel free to leave the comments on LinkedIn, Facebook, Twitter or Friendfeed. I’ll find them! Thanks in advance

I had the privilege of presenting at a Science Commons Symposium this past weekend. (What wasn’t so pleasurable was the red eye home and the body ache I am suffering today!) I’m stealing the list of speakers directly off of the symposium page listing

Stephen Friend - Founder and President of Sage, a non-profit research organization that’s revolutionizing how researchers approach the treatment of disease

Peter Binfield – Publisher of PLoS ONE, an innovative online scientific journal and influencial leader of the open access movement

John Wilbanks – VP of Science Commons, an organization dedicated to making it easier to share scientific data and materials

Heather Joseph – Executive Director at SPARC and champion of Open Access

Antony Williams – VP of Strategic Development for the Royal Society of Chemist, Founder of Chemzoo and a leader in the domain of free access chemistry

Jean-Claude Bradley – Associate Professor of Chemistry at Drexel University and pioneer of the Open Notebook science effort

Cameron Neylon – Open Science evangelist, biophysicist and leading advocate of data availability

Peter Murray-Rust – Founder of Blue Obelisk, a group of chemists dedicated to Open Data, Open Source and Open Standards

I knew a number of the speakers personally but met Heather and Stephen for the first time. There was a clear commonality between the speakers and for the audience..that of having access to, and willingly sharing, data and knowledge. Clearly we are all serving the community in our own ways but there is a common frame of overlap in terms of the urgency with which this needs to be done and the big wins that can result from such efforts.  I had met John Wilbanks a number of times but this was the first time I heard him give his talk. For me personally he is a calming voice in regards to terms of licensing and access to data providing a guided tour of the path to the Creative Commons licenses. He introduced a particular statement that fits with ChemSpider  “..the goal is the sparking of generative science” and quoted Jonathan Zittrain who said “Generativity is a systems capacity to produce unanticipated change from unfiltered contributions from broad and varied audiences.”.

Boom-boom-pow. Did that ever hit. People have been asking me how is ChemSpider being used and how would I want it to be used. Here’s the answer…I want them to get value from it however they may use it. We cannot foresee all the ways that people might derive value from content on the database. We cannot define how scientists might choose to work together around the information available. There are a myriad of opportunities to discover something of interest on the database and we see a big part of our job to populate the database with data and links to additional information and to provide a searchable hub to access those data. We get emails emoting thanks for helping people to find “XXXX” and we’re happy to know that we helped. As I’ve said many times…there is method in our madness and despite the fact that we know SOME of the ways that our platform can be used it’s the “generativity” that is very exciting and we hope to hear about. That’s the web for you!

My talk from Slideshare is posted below

I am shamelessly lifting this post from the wonderful blog of Cameron Neylon by way of advertising a symposium that will happen at the end of this week. If you are on the West Coast and want to come and hear about the changes going on in the world.

“One of the great things about being invited to speak that people don’t often emphasise is that it gives you space and time to hear other people speak. And sometimes someone puts together a programme that means you just have to shift the rest of the world around to make sure you can get there. Lisa Green and Hope Leman have put together the biggest concentration of speakers in the Open Science space that I think I have ever seen for the Science Commons Symposium – Pacific Northwest to be held on the Microsoft Campus in Redmond on 20 February. If you are in the Seattle area and have an interest in the future of science, whether pro- or anti- the “open” movement, or just want to hear some great talks you should be there. If you can’t be there then watch out for the video stream.

Along with me you’ll get Jean-Claude Bradley, Antony Williams, Peter Murray-Rust, Heather Joseph, Stephen Friend, Peter Binfield, and John Wilbanks. Everything from policy to publication, software development to bench work, and from capturing the work of a single researcher to the challenges of placing several hundred millions dollars worth of drug discovery data into the public domain. All with a focus on how we make more science available and generate more and innovative. Not to be missed, in person or online – and if that sounds too much like self promotion then feel free to miss the first talk… ”

We will shortly be locking down the code for ChemSpider SyntheticPages (CSP) and continue testing prior to our release at the ACS meeting in San Francisco in March. As we have done with ChemSpider over the past three years we look to our users for feedback to enhance the system. We will continue to tweak the code, add functionality, enhance the work flows and, ultimately, enhance the database. We believe that the CSP platform that we will roll out will be a good start but ultimately it will not be the platform that makes ChemSpider SyntheticPages a success, it will be the level of participation.

Participation can come in different forms but let’s draw an analogy with Wikipedia for a moment. MediaWiki is used by thousands or even tens of thousands of people worldwide to populate the worlds best known online encyclopedia with data and information. Relative to many web platforms that are out there I judge that MediaWiki, as functional and as well-used as it is, is not a “glitzy platform”. It’s not particularly fancy, some would say rather plain, but it is the foundation of housing the world’s knowledge for all to share in. One of the main reasons Wikipedia is so successful is that the mission they have is appropriate and an enormous community of contributors have participated in adding articles, performed fact-checking, validating references and expanding the coverage of the content.

Both ChemSpider and ChemSpider SyntheticPages are platforms. But clearly ChemSpider wouldn’t have much value to the community, would not be answering many questions for its users, or wouldn’t receive the acclaim from our community were it not populated with data, information, links and content of value. While we have obviously done a lot of heavy lifting ourselves over the past 3 years we owe a debt of gratitude to the growing community of users who have been depositing new structures, spectral data, links to articles and so on. We thank those users who have been curating data, removing erroneous data and relationships. ChemSpider is a much better resource as a result.

When ChemSpider SyntheticPages goes live we will go live with a series of synthesis procedures from the original SyntheticPages.org site. Our intention is to also add in other procedures from journal articles and other sources. Our hope is to build a rich public resource for synthetic chemists with many tens of thousands of validated syntheses. We will add on the semantic markup capabilities and linking to ChemSpider to provide a linked platform. While we will be able to expand the database we are looking to the community to help us. This is a call to action to you, the community.

If you are a synthetic chemist we want your contributions. If you are a chemical vendor making chemicals your contributions to the community via the CSP platform can be invaluable. Whether you are an academic researcher, a government researcher or an industrial researcher, if you have published your syntheses in the literature please add them to ChemSpider SyntheticPages. If there are example syntheses that you have repeated from the primary literature, from some other database or blog, then deposit your data to CSP. We are interested to know whether you will be willing to contribute to our project so let us know on this blog or email us at supportATchemspiderDOTcom. We need your help to make CSP the world’s richest resource of free synthetic procedures online.

We are presently running ChemSpider SyntheticPages Beta off of our servers in Washington DC. Last week the servers were taken offline for a few hours after the 30″ snowfall felled some power lines in the city. Our apologies. There is another storm due to hit Washington this week and an expected 20″ of snowfall. It is possible that our beta servers will go offline again. If that happens we apologize in advance. We are presently configuring our beta servers to run out of the RSC offices in Cambridge in the United Kingdom. When that happens we will be less susceptible to such power issues.

I was sitting down today to review what presentations are coming up in the next few weeks and how much writing and travel was ahead of me. Ugh. Painful. During the next few weeks of conference season there will be a lot of talks and, as usual, a lot of late nights before the presentations to write new talks or modify existing talks. I will be at the ACS meeting in San Francisco this spring and will be giving four presentations, a poster and leading a training session on ChemSpider. The presentations are outlined below. Looking forward to seeing you there and it would be great to hear from any of you who would like to get together and connect about community chemistry over a coffee.

Presentation: Utilizing ChemSpider as a platform for education and exposure of student data to the community.

Educators and students now have access to rich internet resources of information. RSC’s ChemSpider is a community resource of structure-based chemistry delivering data including chemical compound collections, reaction synthesis procedures, physicochemical property and various forms of spectral data. ChemSpider offers the opportunity for the community to participate in populating, annotating and curating the data on ChemSpider. We believe that ChemSpider offers an opportunity for educators and students to participate in the ongoing development of a rich resource for the chemistry community. This presentation will suggest some potential uses of the ChemSpider website in terms of integrating into lesson plans. We will also outline how students can expose their structure and reaction-based research work via the ChemSpider platform for the benefit of the community and their online scientific reputation.

Presentation: ChemSpider – How An Online Resource of Chemical Compounds, Reaction Syntheses, and Property Data Can Support Green Chemistry

ChemSpider is an online database containing in excess of 20 million chemical compounds and associated experimental and predicted physicochemical data, reaction synthesis details and analytical data. A significant amount of the data contained within the database has been harvested and collated from a number of inventory systems and integrated to provide a centralized resource for the community. The ChemSpider database has the added benefit of being available for community deposition, annotation and curation. As a result it offers the potential for researchers to share their latest research with the public and participate in the creation of a rich resource of chemistry related information for the Green Chemistry community. This presentation will provide an overview of present capabilities and discuss the future vision for the platform.

Presentation: ChemSpider, how a free community resource of data can support teaching NMR spectroscopy

ChemSpider is an online database of chemical compounds, reaction syntheses and analytical data. Provided by the Royal Society of Chemistry, our intention is to provide a free internet resource of chemistry related data for the community. ChemSpider is unique in its role of allowing user depositions of chemical structures, synthesis procedures and analytical data and, in so doing, provides an environment for crowdsourced gathering of information. To date over 2000 1D and 2D NMR spectra have been deposited online by the community and are available for reuse. The data have been used as the basis of a spectral game whereby students can learn NMR by interacting with the data. This presentation will provide an overview of the tools and capabilities presently available on ChemSpider to support teaching NMR in the undergraduate curriculum and will outline how the community can participate in enriching this resource for the benefit of all.

Presentation: Enhancing discoverability across Royal Society of Chemistry content by integrating to ChemSpider, an online database of chemical structures

The ability to query across a chemistry publishers content using chemical structure searching can dramatically enhance discoverability. RSC has been applying a number of procedures to integrate RSC’s ChemSpider community resource with our published content and databases. These include: 1) entity extraction procedures 2) chemical name conversion procedures using software algorithms and curated dictionaries 3) semantic markup and 4) a crowdsourced curation processes. This presentation will provide an overview of the processes we have utilized in order to provide structure-based integration to RSC content. We will discuss our ongoing efforts to extend the approaches to the mining of data from the rich supplementary information sections of many RSC publications. Our intention is to provide access to synthesis procedures and analytical data and further enrich the ChemSpider database for the benefit of the chemistry community.

Poster: Utilizing ChemSpider as a platform for education and exposure of student data to the community

Recently I announced the release of ChemSpider  SyntheticPages. We are honored to have an editorial board of chemists to assist in directing the project and they are introduced below:

I’m happy to announce ChemSpider SyntheticPages. We are releasing as a beta for the present and in READ-ONLY mode. Shortly we will release a version that allows you to deposit your own procedures (together with documentation and a couple of training videos). We are out to create a major resource for chemistry in terms of synthetic procedures. We welcome you to use, contribute and participate. Please note that this is a beta and even though we are hoping for only minor issues all feedback is welcomed. Enjoy!

ChemSpider and SyntheticPages announce collaboration supporting synthetic chemistry

CAMBRIDGE, United Kingdom., February 2nd, 2010 – The Royal Society of Chemistry (RSC) today announced the release of ChemSpider SyntheticPages^beta – a community resource of reaction synthesis procedures.

The launch of a beta site is the result of a collaboration between ChemSpider (the foremost and free online structure centric community for chemists) and the original SyntheticPages (www.syntheticpages.org). The partnership, which sees ChemSpider host the content from SyntheticPages, furthers their jointly held missions: to provide rich, high quality chemistry resources for the synthetic chemistry community.

A search of ChemSpider SyntheticPages^beta allows identification and detailing of the experimental procedures for the synthesis of specific chemical compounds. The database has been seeded with SyntheticPages.org data and will be expanded by inclusion of data from journal articles published by RSC. Researchers will also be able to deposit their own synthetic procedures to the site.

Using online semantic markup technologies and integrating to the ChemSpider database will allow interactive display of chemical structures, spectral data and a multitude of related data. Scientists can comment upon a growing resource of interactive synthetic processes, while leveraging the rich resources contained within the ChemSpider databases.

“We are very pleased to partner with SyntheticPages to provide a reaction database for the community. Students, teachers and researchers will have access to a free, highly curated database of synthetic procedures populated by curated depositions from the community and abstracted from RSC publications” commented Dr Antony Williams, Vice President of Strategic Development, ChemSpider.

He added “Our editorial board is made up of active synthetic organic chemists including the original founders of SyntheticPages. Their leadership and guidance will mesh our expertise in web-based technologies supporting semantic chemistry with deep knowledge and understanding of synthetic chemistry.”

Professors Kevin Booker-Milburn (University of Bristol), Stephen Caddick (University College London, UCL), Peter Scott (University of Warwick) and Dr Max Hammond are the original founders of SyntheticPages.

A spokesperson for the group commented “When we started, we believed that there was a place for an interactive database which would allow synthetic chemists who carry out reactions, to find procedures that work. Our aim is to develop a web-based resource that will be on every synthetic chemists’ desktop, and will be regularly used by experimentalists over the world. Our early work has set the stage to achieve this goal and we look forward to the collaboration with ChemSpider to develop a resource that will help sustain high quality synthetic chemistry worldwide”.

“We are particularly grateful to CEM Microwave Technology UK without whom we could not have developed SyntheticPages. We are also grateful to our thousands of members and users who have helped sustain the SyntheticPages endeavour and we look forward to even greater success with ChemSpider.’’

ChemSpider SyntheticPages^beta is released in beta form for feedback from the community at www.chemspider.com/syntheticpages .

For more information contact:

Dr Antony Williams
VP Strategic Development, ChemSpider
Royal Society of Chemistry
Thomas Graham House, Science Park, Milton Road
Cambridge CB4 0WF, UK
Tel: +1 919 201 1516
Email: williamsa@rsc.org

Notes for Editors

About the Royal Society of Chemistry

The Royal Society of Chemistry (RSC) is the largest organisation in Europe for advancing the chemical sciences. Supported by a worldwide network of 45,000 members and an international publishing business, our activities span education, conferences, science policy and the promotion of chemistry to the public.

www.rsc.org

About ChemSpider

ChemSpider offers a structure centric community for chemists to resource data. Offering access to almost 21.5 million unique chemical entities from over 200 data sources and by providing a platform for crowd sourced deposition, annotation and curation, it is the richest source of integrated chemistry information available online. ChemSpider delivers data and services to enable the semantic web for chemistry.

www.chemspider.com

About SyntheticPages

SyntheticPages is a freely available interactive database of synthetic chemistry for the dissemination of practical and reliable organic, organometallic and inorganic chemical synthesis, reactions and procedures deposited by synthetic chemists. Synthetic methods on the site are updated continuously by chemists working in academic and industrial research laboratories. Synthetic pages encourages submissions from graduate students, postdocs, industrialists and academics.

I’m Aileen Day and I’m one of the Royal Society of Chemistry’s Informatics team who are working with ChemSpider. We can loosely be defined as chemists who have picked up enough computer programming to make our lives and those of people around us a bit more exciting and less tedious. Our job is to develop new tools to help viewers and authors of articles in our journals, and our publishing editors. Probably the most high profile example of these tools is the development of Project Prospect.
So the long-term plan for us and ChemSpider is to fully integrate Prospect (and RSC publications) with ChemSpider so that a user can seamlessly bounce back and forth between finding compounds of interest using the ChemSpider search and selection tools and finding more information about them in our journals amongst other sources. Also, to improve the functionality of and content of everything we can along the way (ChemSpider, Prospect etc.).
As a first step of this I’m currently developing a way to automatically deposit the primary (most important) compounds in our prospected articles into ChemSpider, with publication information about the RSC article, including a link back. I’ll keep you posted as we make progress…

We mailed out the first issue of the ChemSpider Newsletter in January which was packed with info on what’s happening with ChemSpider and tips on how you can get the best out of ChemSpider. To make sure you receive your personal copy of future issues by email please make sure to register.