Archive for the ChemSpider SyntheticPages Category

The functionality of electronic lab notebooks (ELNs) and that of ChemSpider overlap to a certain extent – both store chemical information including structures, data, spectra and reactions. However, the focus of most ELNs is to manage, track and audit that data, and that of ChemSpider is to publish and disseminate it to the world. We have been considering how best to use this complementary functionality to integrate an ELN with ChemSpider.

Some ELNs already currently look up information and link to ChemSpider. For example the blog3 Web-logging (“blogging”) engine by Jeremy Frey, Simon Coles and Mark Borkum at Southampton University, which allows links to compounds from the ChemSpider database to be embedded directly into the content of a post. When a link to ChemSpider is detected, blog3 follows the link to retrieve additional information that is relevant to the compound, including: experimental and theoretical data; two- and three- dimensional depictions; and links to papers and journal articles. Another example is the eScience tool that Stephen Wan from CSIRO has developed with the University of New South Wales to text mine LabTrove ELN blog posts to identify chemical names and link these to the relevant ChemSpider compounds.

At the meeting “The Smart Laboratory: Towards a national ELN” meeting (organised as part of the Dial-a-Molecule EPSRC Grand Challenge) in August this year, the seeds were sown to take the integration between ELNs and ChemSpider a step further. Cambridge University has the first Chemistry department in the UK to roll out a department-wide Electronic Lab notebook system, and the software that they’re using is IDBS’s E-WorkBook Suite. In collaboration with IDBS and Cambridge’s Chemistry department, we at ChemSpider have made a plug-in which could both dynamically retrieve information from ChemSpider into their ELN, and publish to it the other way. The Chemistry department at Cambridge (Dr Tim Dickens, Dr Brian Brooks, Prof Bobby Glenn and Prof Steven Ley) have been very helpful in granting access to their ELN to write the plug-in, and will be its first users, but the results will be freely available for any existing IDBS E-WorkBook suite user.

About the extension Prof Bobby Glenn has said: “Much of Chemistry is lost, it is simply not published and languishes in forgotten lab notebooks. Capturing novel molecules soon after synthesis on a searchable database like Chemspider is now an effortless process directly from the ELN, which will greatly encourage sharing of compounds, synthetic methods and all the associated data. It’s instant messaging for chemists”. Antony Williams (Vice-President of Strategic Development of ChemSpider) added “The ability to now publish compound data from the IDBS ELN directly to ChemSpider offers a path to direct exposure of novel chemistry as well as the chemist doing the work. This public compound registration capability is the first move towards ultimately exposing synthetic methods and associated experimental data to the community. Our vision is coming to fruition through this collaboration.”

To view the plug-in in action please view the demonstration movie of ChemSpider E-WorkBook Suite Plugin.

Screen capture of launching Publish to ChemSpider plug-in

Compounds can be published to ChemSpider if they have been drawn out in full in an experiment – whether this is as an individual structure or part of a reaction, and whether they are simply uploaded into the experiment as a reaction file, or included in for example a spreadsheet item. Likewise, compound structures can be automatically loaded into a search of ChemSpider if you would like to find out more information about compounds that have been drawn out in full in an experiment, or if you have published a compound to ChemSpider and wish to see the resulting compound pages. The resulting compound pages in ChemSpider will have the data source “IDBS E-WorkBook Suite”. The external ID will show the ID of the experiment from which the structures are from, and the depositor details as defined in the ChemSpider Settings of the ELN.

The ChemSpider IDBS E-WorkBook Suite plug-in is freely available to customers of IDBS E-WorkBook Suite by downloading it from IDBS, and copying it the appropriate place in their IDBS E-WorkBook Suite program files. It is compatible with E-WorkBook Suite versions 9.0 and 9.1.

This plug-in is an initial proof-of-concept to demonstrate that we can pass compound information between ChemSpider and an ELN in both directions. Future versions will allow more of the information within an experiment to be published to ChemSpider – for example to allow reactions along with a description of their methods to be published to ChemSpider SyntheticPages, or to deposit spectra along with compounds to ChemSpider. We would also like to integrate other ELNs with ChemSpider.

If you are an iPhone user (as I am), have an iPad hanging around to check email 20/7 (I have to sleep sometime…), or use a phone with a browser, I suggest you point it to the new ChemSpider Mobile at  http://cs.m.chemspider.com. There you’ll see a simple interface, shown below, that allows you to search across our database of almost 25 million chemical entities based on chemical name (systematic, trivial or trade, registry number etc) and retrieve a list of intrinsic properties, a list of predicted properties, a list of associated identifiers, with links to Wikipedia if available, and a Google based search for the chemical based, for now, on the associated InChIKey. Check it out, give us feedback.

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.

iphone1

iphone3

iphone4

iphone5

When ChemSpider SyntheticPages is formally released at the American Chemical Society meeting next week at the Spring National Meeting in San Francisco we will also introduce both the ability to structure search ChemSpider SyntheticPages as well as show a snippet of the reaction in ChemSpider itself. We have introduced a new reaction Infobox and display the snippet of the reaction based on compounds marked as primary reactants or products in the SyntheticPages article.

For example, see the reaction infobox for this record.

CSP

The functionality discussed below will be released at the ACS Spring Meeting during the week of March 21st 2010

The Royal Society of Chemistry has a whole series of databases. None of them have been structure searchable…until now. As with our PubMed integration and our Google Patents integration rolling out shortly, just because a database hasn’t had the chemical structures extracted and indexed doesn’t mean that those resources cannot be made “structure searchable”. It’s not a subtle distinction however, as discussed in the Google Patents blog post. These types of integrations depend on the correct association between chemical names and structures, access to an API allowing facile and flexible searching and, something that is purely serendipitous in nature, the absence of overlaps between chemical names and common language.

We have used the recently announced RSC Publishing beta platform and the API made available to us to enable the searching. As my colleague Graham McCann announced recently “(the) platform gives access to over 500,000 journal articles, book chapters and database records through one simple search interface. The new platform delivers faster browsing, intelligent searching and more intuitive navigation and is open for beta testing now.”

Our approach has been to search the title and the abstract for each of the databases for all of the validated identifiers. It works. It is FAST and it provides “structure-related” access to all six RSC databases. An example screen shot is below where a search on chlorobenzene retrieves data on each of the following databases: Mass Spectrometry Bulletin, Laboratory Hazards Bulletin, Methods in Organic Synthesis, Catalysts and Catalysed Reactions, Natural Product Updates and Analytical Abstracts. The screen shot below shows the analytical abstracts linked by the term chlorobenzene in the title or abstract itself. 284 hits..in a fraction of a second. The abstract is linked out to the original article via DOI, where possible.

databases

My personal favorites in the set of databases are the Natural Product Updates (NPU) and the Methods in Organic Synthesis (MOS) databases. The NPU database contains tens of thousands of natural product chemical structures, together with chemical names, references and some physical properties. Rich resources for ChemSpider. MOS includes includes reaction schemes, title and bibliographic details. Rich resources to connect to ChemSpider SyntheticPages in the future.

We have only just started to tap into the riches contained within the RSC archive. It’s like stumbling across a roomful of rubies to pick up diamonds. There is content all around us waiting for us to connect. We will connect this up to ChemSpider and make it available. Access to the databases will be shown at the ACS Meeting in San Francisco.

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.

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 SyntheticPagesbeta – 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 SyntheticPagesbeta 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 SyntheticPagesbeta 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.