Earlier this month I reported on the integration of Infotherm to ChemSpider but at that time it would have been necessary for non-RSC members to pay for the data on Infotherm despite the fact that a search would have provided the links and you could have clicked through to the Infotherm data pages. Some good news from Fiz-Chemie though…they are waiving the fee for data on pure compounds accessed from ChemSpider and as a result giving access to over 200,000 tables of data. This is a great contribution to the community of ChemSpider users. Thanks Fiz-Chemie!

 

infotherm

Last night I gave a presentation at the BAGIM meeting in Boston. The abstract is below together with the embedded presentation from Slideshare

ChemSpider – Is This The Future of Linked Chemistry on the Internet?
ChemSpider was developed with the intention of aggregating and indexing available sources of chemical structures and their associated information into a single searchable repository and making it available to everybody, at no charge. There are now hundreds of chemical structure databases such as literature data, chemical vendor catalogs, molecular properties, environmental data, toxicity data, analytical data etc. and no single way to search across them. Despite the diversity of databases available online their inherent quality, accuracy and completeness is lacking in many regards. ChemSpider was established to provide a platform whereby the chemistry community could contribute to cleaning up the data, improving the quality of data online and expanding the information available to include data such as reaction syntheses, analytical data and experimental properties. ChemSpider has now grown into a database of almost 25 million chemical substances, grows daily, and is integrated with over 400 sources, many of these directly supporting the Life Sciences. This presentation will provide an overview of our efforts to improve the quality of data online, to provide a foundation for a linked web for chemistry and to provide access to a set online tools and services to support access to these data.

When you’re viewing a compound page in ChemSpider e.g. hydrogen peroxide there are several ways to find more detailed RSC information (articles and books) about that compound:

  1. In the “Articles” infobox, the results under the “Links & References” tab are links to various journals that have either been deposited or added by ChemSpider users. When the RSC enhances one of its articles, the most important compounds in the article are submitted to ChemSpider for deposition (see here for more details), and when this happens, the article details are also deposited so that a link will appear in this box. As such, there usually won’t be thousands of links in this box, but those that are there will for example pick up references to compounds which maybe aren’t named explicitly in the article (but for example are drawn out in a figure) and as such couldn’t be found by a simple text serach.
  2. The results under the “RSC Journals” tab in the “Articles” infobox are the results of passing a search into the RSC publishing platform to retrieve all of the journal articles that contain any approved synonym for the compound (in the “Identifiers” infobox under the “Names and Synonyms” tab). Since these lookups first appeared in ChemSpider 6 months ago (see here for more details) this platform has progressed from bring a beta version, to now being the fully-fledged publishing platform for searching on and delivering RSC journals, books and databases. To investigate the functionality of this platform more and refine your search results list, click on the link above the list of results to “Click here to explore results” and this will allow you to sort the results by date, or apply filters e.g. to restrict the results set by author, date range,  journal etc.). This is useful since for common chemicals, the list of results returned can be long.
  3.  The “RSC Books” tab under “Articles” performs a similar search on occurences of the approved synonyms but on RSC books rather than RSC journal articles.
  4. Likewise, the “RSC Databases” infobox shows search results of the same approved synonyms but this time the results are from the various RSC abstract databases named in its various tabs. This means that they contain references to the compounds in non-RSC articles.

Links to RSC Articles

We deposit a lot of data onto ChemSpider in a  month and the database is growing daily. As an example of the ongoing depositions take a look at what has been deposited in a one month timrframe from July-August. This is simply what has been published by me…not all depositions. It’s a pretty good indicator of ongoing efforts to enhance the quantity of content on the site.

published_in_a_month

The Chemicalize website from ChemAxon is gaining interest (1,2) and, likely, LOTS of users! Chemicalize is both a website for recognizing chemical names and converting to chemical structures as well as an integration path to their property prediction algorithms. Some basic testing of chemicalize shows that their chemical name detection and conversion to structures using either name to structure conversion (algorithmically) or name lookup (via dictionaries) is very good. Not perfect, but very good. Perfect chemical name lookups are impossible as the associated dictionaries grow every time a new natural product is found for example, or a new drug is released.

With ChemSpider we are more interested in the linking to the predicted property pages. For example, if you want to see the predicted properties for Penicillin visit here.

penicillin

Now, with ChemSpider ChemAxon were kind enough (and I mean applaud them, acknowledge them and send flowers!!) to give us a way to pass through a structure and initiate the predictions on the Chemicalize site. This is tremendous news for you all! Under the properties Infobox we provide a list of properties from ACD/Labs, a list of properties from EPISuite, a list of experimental properties, sourced from various places and now, the link to Predict Properties using Chemicalize.

properties

Clicking the tab for Predict Properties from ChemAxon display the link through to Chemicalize as shown below.

chemicalize So, now we have sets of prediction capabilities linked up to ChemSpider. The ACD/Labs predictions are pre-calculated and every time there is an update to the algorithms in theory we would have to recalculate across the database and publish. This would take weeks of time across the almost 25 million structures so it is not a frequent task. It is the same issue with EPISuite. With the Chemicalize integration however the predictions are live, on the structure at the time it is passed to the algorithms. This has the advantage that the prediction algorithms can be incrementally improved and you will always get the latest and greatest results. However, having the predicted values from ACD/Labs available allows flexible searching as shown below. We are grateful to ChemAxon to allowing us to integrate Chemicalize. It gives LIVE access to the latest and greatest predictions as well as access to a whole series of new predictions for which we don’t have data on the database…especially pKa values, topology analysis, geometry and others. Thanks ChemAxon!

acdlabs

It’s a while since we first started the ChemSpider Forum and things have been a little quiet there recently as we made the transition to RSC ChemSpider, so we would like to invite you to re-visit the Forum and share your comments, suggestions and ideas with us.

On the newly revamped ChemSpider website you will find a link under the Help menu that will take you directly to the Forum.

Share some of your user experiences: How do you use ChemSpider? What problems did it solve for you? Did you look for something and didn’t find it?

The Forum will also be a place to find documentation such as Quick Guides on How to do Searching on ChemSpider and How to Add structures, spectra or reactions to ChemSpider so you can help to grow the community for chemistry.

We look forward to hearing from you.

Laying out intrinsically three-dimensional molecular structures in a readable way on a two-dimensional page is a hard problem for human beings, let alone for algorithms, which is why ChemSpider stores a 2D layout alongside the InChI, which only describes which atom is connected to which other atom.

This is a really valuable resource for enhancing our RSC journal articles, so we’ve been experimenting with adding galleries to compounds, with examples here and here. Is this what PDFs you download from the website should look like? Would a digest gallery of the latest articles published be more useful? Do let us know.

As this is my first posting on the ChemSpider blog I should introduce myself. I’m Colin Batchelor and I’m in the Informatics team at the RSC. Some of my work is on ChemSpider, but I also work on informatics for RSC Publishing, and I’m a member of the InChI subcommittee.

PubChem is a very large source of compound structures and data, but the quality and reliability of these can be variable. However, within it, some sets of compounds and substances could be trusted more than most because they’ve been deposited by reliable data sources – for example those deposited by the Nature Publishing Group that correspond to compounds in Nature Chemistry, Nature Communications and Nature Chemistry Biology articles.

We have developed an automated method to search PubChem for substances deposited by the Nature Publishing Group, to extract their structures and properties in sdf format and then import them into ChemSpider. The result is a newly imported set of 5525 molecules in Chemspider. These compounds were deposited in PubChem since 2005 and originate from over 400 articles. All imported compounds link back to the original article – see below.

Example compound from PubChem

The process is automated and can be scheduled to scrape PubChem for newly deposited compounds, and stream these into ChemSpider so this subset will be updated regularly.

This initial prototype could pave the way for other high quality, consistently formatted subsets of PubChem to be identified and deposited into ChemSpider in a similar way. To suggest other possible subsets of PubChem which could be used by ChemSpider join the discussion on the ChemSpider forum.

With one week to go before the American Chemical Society meeting we have unveiled the new ChemSpider website for feedback and comments.We believe that we have made the site easier to navigate, more visually appealing and faster to navigate. The new site map should be very helpful in navigating the site.

We are presently gathering feedback from users with different browsers, updating some of our documentation and generally optimizing performance and navigation across the site. All feedback is welcomed…we’d love to hear from you!

website_redesign

Have you ever had a niggling feeling that you’ve been missing some corner of ChemSpider which might have a tool that will make your life much easier?

http://www.chemspider.com/Sitemap.aspx is the new sitemap for ChemSpider which lists all of the different pages in it and will help you to get an overview of all the different things that you can see and do on ChemSpider.

There are also brief descriptions about each page which will, where necessary, suggest input examples if you just want to try something out but aren’t quite sure what to type into the boxes. If you are a ChemSpider depositor or curator and view the sitemap when logged in you will see additional pages relevant to your assigned roles.

There will be two presentations and a training session about ChemSpider at the ACS meeting in Boston. We hope to see you there if you are attending the meeting. In any case the presentations will be uploaded after the conference onto the SlideShare site.

The presentations are:

Chemistry in your hand: Using mobile devices to access public chemistry compound data, August 26, 2010 1:30 pm, Boston Convention & Exhibition Center, Room: Room 156A

 

How community crowdsourcing and social networking is helping to build a quality online resource for chemists, August 22, 2010 10:25 am, Seaport Hotel, Room: Seaport Ballroom A

The training session is detailed below:

“An Overview and Update of RSC-ChemSpider Capabilities”

Tuesday, August 24, from 3:30-6pm,  Boston Convention and Exhibition Center, Room 102B

The Fall American Chemical Society meeting in Boston is just around the corner and we are finishing up the integration of some recent developments. As is usual we have way more things that we wanted to deliver than we have been able to implement. But we’ve always got more ideas so this is no surprise. The biggest change is the new website redesign that a number of readers of this blog voted on and influenced. In the next few days I will announce new features and integrations that we will be delivering, all being well!

Pillbox is defined on the website as “…enables rapid identification of unknown solid-dosage medications (tablets/capsules) based on physical characteristics and high-resolution images.” I first heard about PillBox when David Hale, “host” of Pillbox, and I were on the same speaking agenda at a meeting in Washington. David is a very engaging speaker and I really appreciated the visual nature of what they are working to deliver. Trying to identify the pharmaceutical ingredients in a pill from the color and pill imprint etc is tough…then comes PillBox.

Using the API provided to PillBox we have integrated ChemSpider directly to PillBox. So, in the future when you search on Viagra on ChemSpider and find Sildenafil Citrate you will see a new link to Pillbox (we are determining where on the page at present) and under there you will see the links to Pillbox.

A search on Viagra on Pillbox will show this:

pillbox1

but using the API we can show the information embedded into the ChemSpider page as show below.

pillbox2

Notice that all three Viagra dosages are shown and each can be opened to preview one at a time. 

This is simply one more example of integrating into the online resources becoming increasingly available and focusing on having ChemSpider being a structure-searchable hub connecting them together.

iChemLabs, the developer of the popular ChemDoodle chemical drawing program, and Royal Society of Chemistry’s ChemSpider, a leading provider of chemical services and data on the internet, are excited to announce a software agreement that will provide significant benefits to customers.

iChemLabs, a developer of chemical software for students and professionals, announces a strategic partnership with RSC ChemSpider. iChemLabs has integrated ChemDoodle with the ChemSpider database containing almost 25 million compounds to search for pre-drawn chemical structures through the innovative MolGrabber widget. ChemSpider is integrating ChemDoodle Web Components into their service to provide users with a next generation HTML5 experience.

Search ChemSpider with ChemDoodle

Kevin Theisen, President of iChemLabs, states “ChemSpider is an excellent example of the creation of a popular and useful service by utilizing cutting-edge technology. By incorporating the HTML5 ChemDoodle Web Components, ChemSpider will take a further step towards creating the most advanced and futuristic chemical database on the web. Now that ChemDoodle Web Components are fully supported on iPhone OS and Android, our partners will be able to push rich media services to their customers across all browsers and mobile devices.”

Antony Williams, VP of Strategic Development for ChemSpider, adds “For many chemists ChemSpider has become their primary website to search for chemicals and related information, whether it be through a standard browser or via a mobile device. Our intention is to offer the best user experience possible and integrating to the HTML5-compliant ChemDoodle Web Components will afford users enhanced capabilities.”

ChemDoodle is available for download immediately. New users can request a free 30 day trial at http://www.chemdoodle.com. The free and open source ChemDoodle Web Components can be accessed at http://web.chemdoodle.com. ChemSpider is hosted at http://www.chemspider.com.

About iChemLabs, LLC.:
iChemLabs, LLC. is a scientific software company specializing in all forms of computational chemistry including NMR simulation, chemical visualization, and chemical informatics. iChemLabs provides expertise in desktop, mobile and web based technologies for both consulting and custom development. www.ichemlabs.com

About the Royal Society of Chemistry:
The RSC is the largest organisation in Europe for advancing the chemical sciences. Supported by a worldwide network of 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 25 million unique chemical entities from over 400 data sources and by providing a platform for crowd sourced deposition, annotation and curation, it is the richest source of free integrated chemistry information available online. ChemSpider delivers data and services to enable the semantic web for chemistry. www.chemspider.com

Name Kevin Theisen
Phone 888-505-2436
Email sales@ichemlabs.com
Url http://www.ichemlabs.com
Address 200 Centennnial Ave., Suite 200
City/Town Piscataway
State/Province NJ
Zip Code 08854
Country USA
   
Name Antony Williams
Phone 919-201-1516
Email info@chemspider.com
Url http://www.chemspider.com
Address 904 Tamaras Circle
City/Town Wake Forest
State/Province NC
Zip Code 27587

The INFOTHERM® database, produced by FIZ CHEMIE  Berlin, has now been linked into records in ChemSpider.

The database provides experimental thermodynamic and physical properties of 33,000 mixtures and 9,000 pure substances from a total of 12,000 compounds. In ChemSpider if you search for a compound and look under the Phys. Properties tab in the Associated Data Source Info box, you will find a link to a record in INFOTHERM.

ChemSpider record for Artemisinin showing INFOTHERM link

ChemSpider record for Artemisinin showing INFOTHERM link

Clicking on the ID link will take you to records in INFOTHERM for that compound where you can look at the various thermodynamic properties available and make a selection of which property is of interest. By clicking on the button for Full access you can view the experimental data and find a link to the bibliographic reference.

 

Artemisinin's solubility in supercritical carbon dioxide

Artemisinin's solubility in supercritical carbon dioxide

I have been at the BCCE conference here in Dallas for two days. I gave two talks in a session hosted by Harry Pence and Bob Belford, participated in their workshop on Social Networking and spoke about how to set up a blog and my experiences of blogging and today led a workshop on Online Public Compound Databases. Today was 3 hours of discussions, an agenda that was strict enough to keep us on focus but free enough to allow lots of questions and real time web-based searching. I really enjoyed the challenge of the session in terms of discussing the challenges of teaching web-based literacy in searching for chemistry online. The Powerpoint aspect of the presentation is on Slideshare below

A few weeks ago we won an award from Bio-IT World for Community Service. Allison Proffitt from Bio-IT world interviewed me recently in connection with the award and some of the history behind ChemSpider and wrote it up for the magazine. The resulting article is also available online here.

We are in the process of a website redesign with the intention to deliver a new look and feel in time for the ACS meeting. We have some draft pages available online and we would like YOUR feedback please!

We have five drafts of the Home page that we would like your comments on. Let us know which one is your favorite by giving us the number of your favorite when you comment as well as any other comments.

Home Page 1

Home Page 2

Home Page 3

Home Page 4 (static image)

Home Page 5 (static image)

The draft of our Chemical Record page is here:

Chemical Record Page

Comments and feedback welcome!

Richard Kidd

We’re very proud that ChemSpider is one of the shortlisted finalists for the ALPSP 2010 Publishing Innovation award – the other finalists are Mastervision from DataSalon, Semantic Biochemical Journal from Portland Press, and UniPHY from the American Institute of Physics. The winners will be announced on 9 September at the ALPSP International Conference, so good luck to all, fingers crossed here and we’ll let you know the result.

First post for me on the ChemSpider blog, so a quick introduction. I’m Richard Kidd, and I manage the Informatics team at the RSC in Cambridge. We work on the technical enhancements of our publications (such as 2007 ALPSP Innovation award winner RSC Prospect) and we’re supporting the current and future ChemSpider developments alongside the original team – and this also includes support for ChemSpider users and depositors. We’re all here.

It is now a year since the Royal Society of Chemistry (RSC) acquired ChemSpider and much has happened in what is really  quite a short space of time.

ChemSpider has added more compounds and data sources, significant compound collections, there are now links to RSC Publishing and PubMed which are effectively making these resources structure-searchable, we have set-up a micro publishing platform with the development of ChemSpider SyntheticPages and we have facilitated mobile chemistry with the launch of  ChemSpider Mobile.

We are impressed with these developments and we hope you are too. We are always interested to hear your views.

Look out for even more new features which will be released shortly.

If you are attending the Fall ACS Meeting in Boston, August 22-26 you can learn more about all of these developments and more by attending an interactive workshop which is being held on Tuesday, August 24, 3:30 PM – 6:00 PM in the Boston Convention & Exhibition Center, Room 102B. Register now.

You could also attend one of the lectures being given by Antony Williams:

How community crowdsourcing and social networking is helping to build a quality online resource for chemists – August 22, 2010 10:25 am
LOCATION: Seaport Hotel, Room: Seaport Ballroom A

Chemistry in your hand. Using mobile devices to access public chemistry compound data – August 26, 2010 1:30 pm
LOCATION: Boston Convention & Exhibition Center, Room: Room 156A

 We look forward to seeing you there.

15th July 2010.

Today MolPort announces that a connection has been established between its compound procurement module and the Royal Society of Chemistry’s ChemSpider, the structure-centric community for chemists. A link has been created from ChemSpider to MolPort so that ChemSpider users can readily order rare chemicals for their research identified through ChemSpider’s website.

The Internet is an ever-growing resource for chemical information. But searching it for chemical compounds has been inefficient because of the difficulty of searching via conventional search engines. To overcome this problem, ChemSpider has built an aggregation and search service that links to more than 300 information sources: patent information, scientific literature, public databases and web resources. ChemSpider also provides unique community features that allow users to correct information on the website and add additional resources.

However, even if chemists are able to find the information they need on a rare chemical using resources like ChemSpider, they are often unable to readily order the compound. Even if researchers are able to locate a supplier, the ordering process still often takes rounds of communication and is very time consuming. By integrating with ChemSpider, MolPort’s centralized ordering service for rare chemicals reduces these chores to a minimum; for example, compounds from multiple suppliers can be obtained with a single order through MolPort.

Suppliers are rated for their reliability and service on MolPort’s website by users. Researchers can review a list of potential suppliers and their performance before picking a supplier rated with the best customer service and placing orders with the chosen supplier. By joining forces with resources like ChemSpider, MolPort serves as a one-stop shop for researchers seeking rare chemicals.

MolPort CEO, Imants Zudans Ph.D., commented, “We are excited about the integration of information between MolPort and ChemSpider. We anticipate that the connection between the two websites will improve the online experience of a researcher searching for information about specific and rare chemicals, improving their productivity and effectiveness.”

Antony Williams, VP of strategic Development for ChemSpider at RSC added, “MolPort addresses a common need for the users of ChemSpider, that of helping to source a particular chemical. Our focus is on delivering functionality and integrations on ChemSpider to facilitate chemists in their work and the integration to MolPort is a natural extension.”
About MolPort

MolPort is a unique and global chemical compound marketplace for hassle –free, centralized ordering of rare chemicals. MolPort has created a world-class database of commercially available chemical compounds. The free online search portal, www.molport.com, features unsurpassed, advanced search capabilities for chemical structures that are expressly geared for a sophisticated and demanding user.

Contact Details:

Imants Zudans PhD
CEO

SIA MolPort
Smerla iela 3
Riga, LV-1006
Latvia
LV-1006

Email: info@molport.comPhone: +371 67790398
Fax: +371 67801123
About the Royal Society of Chemistry

The RSC is the largest organisation in Europe for advancing the chemical sciences Supported by a worldwide network of members and an international publishing business. RSC 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 25 million unique chemical entities from over 300 data sources and by providing a platform for crowd sourced deposition, annotation and curation, it is the richest source of free integrated chemistry information available online. ChemSpider delivers data and services to enable the semantic web for chemistry. www.chemspider.com

Contact Details:

Antony Williams PhD, FRSC
VP Strategic Development
ChemSpider, Royal Society of Chemistry

Email: info@chemspider.com

RSC Members got to hear all about ChemSpider SyntheticPages in a short article penned by Peter Scott and myself. We also ended up having the cover dedicated to the article. Meanwhile, over at ChemSpider SyntheticPages of late new depositions of syntheses are daily and the database is growing. Here’s hoping we have 500 syntheses online by the time we get to the ACS meeting in Boston!

rscnews

In March of this year I attended the RSC Editors Symposium in Brussels and helped lead a couple of workshops with Richard Kidd about Enabling the Internet for Chemistry. The Editors Symposium is described here. The final report is very interesting in terms of what editors would like to see happen in the future and garnering feedback for our efforts today. The feedback on our sessions, shown below, was overwhelmingly positive. The sessions were fun, interactive and overwhelmingly positive.

D: Enabling the Internet for Chemistry:
ChemSpider and RSC journals

• I was very impressed by the ChemSpider search engine
• A valuable research AND teaching tool.
• The Chemspider workshop was the most interesting which looks to be very useful to the scientific community and I have been greatly encouraged to go away and try it for myself
• I was unaware of the content and use of this software and think it will be an extremely powerful resource
• I also enjoyed the session on ChemSpider and have had a long play on the tool. It has a lot of compounds but unfortunately at the moment not many references which limits its current use
• Although I was aware of ChemSpider, the workshop provided good information concerning the tremendous opportunities for exploitation in teaching and research
• I was also not aware of the power of ChemSpider and will certainly recommend its use to my institution
• The ChemSpider was very interesting as I believe it opens up huge possibilities for the RSC, for example, ChemSpider education, especially for pre-16 year olds which wasn’t addressed
• Very ambitious project; great service of RSC to the scientific community
• Learning about ChemSpider was a highlight as this new source has the potential to make a significant impact in how chemical structures are researched online

ChemAxon have introduced support for both PubChem and ChemSpider into their MarvinSketch canvas. This is in version 5.3.4. We also have fixed and updated the integration with ACD/ChemSketch and Symyx Draw integration is also in place. We are open to integrating to other structure drawing packages if you are interested.

18 June 2010

ChemSpider, the Royal Society of Chemistry’s online chemistry community and database, scooped the Innovative Software Award at the iExpo/KM Forum 2010.

The prize is organised by GFII (the Association for Professionals of the Information Industry) and recognises leading software providers in the information industry for their innovative capabilities and user interfaces.

The organisers, with the intention of promoting the industry of professional information and knowledge management, dedicated the prize for the 16th consecutive year to the most innovative organisations.

Presented by Didier Benard, from Sanofi Aventis R & D, the award recognises a non-commercial initiative in enhancing information online whether for the professional community or for the general public. The jury selected ChemSpider as an award winner for providing free access to data on chemical information (both text and structure-based), which is reliable and controlled by an international expert community.

ChemSpider links together compound information across the web, providing free text and structure search access of millions of chemical structures. With an abundance of additional property information, tools to curate and use the data, and integration to a multitude of other online services, ChemSpider is the richest single source of structure-based chemistry information available online.

Antony Williams, VP of Strategic Development, ChemSpider, said: “The recognition of our efforts to provide the internet’s premier online search engine for chemistry by such a distinguished panel of judges is very flattering. This award further encourages us to remain focused on the delivery of the world’s primary free chemistry portal.”