The RSC’s free chemical database ChemSpider has added RDF functionality to its interface, in collaboration with the University of Southampton’s School of Chemistry. The availability of RDF allows the database records to be found and understood by semantic web tools, another step in ChemSpider’s mission to create a public chemical information infrastructure.

Richard Kidd, Informatics Manager at the RSC says “we are delighted to work with top academic teams pushing forward what’s possible with semantic chemistry, and we hope others will use the RDF representation of ChemSpider to support their own developments”

ChemSpider as a Linked Data source for oreChem

The machine-processable representation was specifically developed in order to leverage the core competencies of the ChemSpider database: resolvable identifiers; high-quality, curated metadata; and rich linking to the extensive RSC corpus. Furthermore, as part of the Microsoft Research-funded oreChem project, OAI-ORE technology is being used to facilitate the discovery and re-use of the chemical information in the correct context.

Prof Jeremy Frey and Dr Simon Coles commented “it is a pleasure for Southampton to work with the RSC’s ChemSpider as a culmination of our contribution to the Microsoft-funded oreChem project. As a member of the Southampton Chemistry eResearch team, this work forms the core of graduate student Mark Borkum’s PhD thesis. ”

“Enabling open, semantic chemistry in this way is a monumental step forward for the domain,” notes Lee Dirks, director of Education & Scholarly Communication for Microsoft Research, “We’re thrilled to have played a role in facilitating the creation of this resource and extremely pleased to see Southampton and the RSC innovating and leading the field.”

Another oreChem participant, Carl Lagoze, the Associate Professor, Cornell University Information Science, Co-Director Open Archives Initiative added “it’s wonderful to see the results of our work on OAI-ORE in this exciting application. It fulfils our goal of making the results of research easier to disseminate and reuse”

Read the rest of this entry »

ChemSpiderman, Antony Williams, will be giving ficve presentations at the #ACS Denver meeting in the fall. The times and dates will be listed when they become available. The list of titles is below.

Structure representations in public chemistry databases: The challenges of validating the chemical structures for 200 top-selling drugs

Chemistry in the hand: The delivery of structure databases and spectroscopy gaming on mobile devices

Aligning scientific expertise and passion through a career path in the chemical sciences

ChemSpider: Does community engagement work to build a quality online resource for chemists?

Identifying “known unknowns” using mass spectrometry data and ChemSpider

It’ll be a different type of talk than most I have given before on ChemSpider…should be fun!

I am happy to announce that ChemSpider is a part of the Open PHACTS project. It is detailed in the following PDF file but can be summarized with the extract from the Wikipedia article I recently posted.

“Open PHACTS is an Innovative Medicines Initiative project aiming to deploy a highly innovative open standards, open access, semantic web approach to address key bottlenecks in small molecule drug discovery – disparate information sources, lack of standards and information overload. It will become an open, integrated and sustainable chemistry, biology and pharmacology knowledge resource for drug discovery. It will provide tools for a comprehensive platform of chemical, biological and pharmacological information, confederated from vast, distributed and variable data and information sources. This semantically enriched and fully interoperable platform will deliver information on small molecules and their pharmacological profiles, including pharmacokinetics and ADMET data as well as on biological targets and pathways. The proposed platform will be a widely accessible, open innovation platform that will serve EFPIA partners as well as biotech and academic drug-discovery for one of their core business activities: knowledge discovery and verification. Practicing drug-discovery scientists in both the public and the private sector will turn to this service to: – integrate data on target expression, biological pathways and pharmacology to identify the most productive points for therapeutic intervention – investigate the in vitro pharmacology and mode-of-action of novel targets to help develop screening assays for drug discovery programs – compare molecular interaction profiles to assess potential off-target effects and safety pharmacology – analyse chemical motifs against biological effects to deconvolute high content biology assays.

The Open PHACTS consortium comprises 23 European core partners, with leading experts in the fields of data mining, annotation, small molecule data storage and manipulation, target related bioinformatics, pathway annotation, protein structure analysis, massive daily in silico reasoning, chemical biology, and computational chemistry. These are: Pfizer, Universität Wien>, Technical University of Denmark, University of Hamburg, BioSolveIT GmBH, Consorci Mar Parc de Salut de Barcelona, Leiden University Medical Centre, Netherlands Bioinformatics Centre, Royal Society of Chemistry, Vrije Universiteit, Spanish National Cancer Research Centre, University of Manchester, Maastricht University, ACKnowledge, University of Santiago de Compostela, >Rheinische Friedrich-Wilhelms-Universität Bonn, AstraZeneca, GlaxoSmithKline, Laboratorios del Dr. Esteve, Novartis, Merck KGaA, Lundbeck, and Eli Lilly.”

The Open PHACTS website can be found here. There will be a lot more details about Open PHACTS in the next few months. Follow the conversation on Twitter here: http://twitter.com/#!/Open_PHACTS

 

 

Dotmatics Limited is pleased to announce that it will provide its web-based structure drawing tool, Elemental, to the leading chemistry community website ChemSpider. Elemental provides a zero install drawing tool that lets users draw simple chemical structures or complex structure queries directly within a webpage.

Antony Williams, Vice President of Strategic Development for ChemSpider comments “Elemental offers ease of deployment and flexibility in structure drawing to our community of users and we are happy to embrace this web-based structure drawing platform as an entry point to the rich resources of ChemSpider.”

Dr Mike Hartshorn, Director and CSO of Dotmatics, said “We are delighted to be working with such a well-known chemistry resource as ChemSpider. The new tools will allow simple access to the wide range of structures and related information that is maintained by ChemSpider and the RSC”.

About Dotmatics
Dotmatics Limited (www.dotmatics.com) is a leading provider of web-based database integration and visualisation tools for use within the life sciences industry.

About the Royal Society of Chemistry
The Royal Society of Chemistry is the UK Professional Body for chemical scientists and an international Learned Society for the chemical sciences with more than 47,500 members worldwide. It is a major international publisher of chemical information, supports the teaching of chemical sciences at all levels and is a leader in bringing science to the public. www.rsc.org

About ChemSpider
ChemSpider offers a structure-centric community for chemists to resource data.  Offering access to over 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

Contacts:
Mike Hartshorn
Dotmatics Limited, The Old Monastery
Windhill, Bishops Stortford
CM23 2ND, UK
Tel: +44 1279 654123
Email: info@dotmatics.com
www.dotmatics.com

Antony Williams
ChemSpider, Royal Society of Chemistry
904 Tamaras Circle
Wake Forest, NC 27587
Tel: 919-201-1516
Email: info@chemspider.com
www.chemspider.com

 

 

Last week Antony Williams gave three presentations about ChemSpider as a chemistry resource at the 241st ACS National Meeting  & Exposition in Anaheim.

For those of you who were not able to attend here are the presentations:

RSC ChemSpider as an environment for teaching and sharing chemistry 

Hosting a compound centric community resource for chemistry data 

How the web has weaved a web of interlinked chemistry data 

In January of this year we held a meeting in London with a group of interested parties who wanted to discuss with us how ChemSpider can be used to support metabolomics. From my point of view that was a very successful meeting in terms of providing an overview of what ChemSpider is capable of today as well as garnering feedback and input from a community of users applying mass spectrometry to perform metabolomics studies.

As a result we will be holding a round-table discussion here in the United States in Research Triangle Park, North Carolina, in April 2011, again for scientists interested in further refining how ChemSpider can be extended to serve the metabolomics community. An outline of the meeting is provided below. If you are interested in participating please respond to me directly at williams”AT”rsc”DOT”org by the deadline listed below. We will cap the attendance fairly quickly and are specifically looking for people who can be vocal about their needs and how we may be able to help with ChemSpider as a platform.

Metabolomics Round Table – Delivering Value to the Metabolomics Community via ChemSpider, a Public Domain Database

Hosts: John Shockcor, Waters and Antony Williams, Royal Society of Chemistry

When: April 21st, 2011

Venue: To Be Determined, Research Triangle Park, North Carolina

The metabolomics community presently utilizes public domain databases such as KEGG, LipidMap, DrugBank and a myriad of other online resources to assist in the analysis of data. However, rich as these resources are, they are limited in scope, are challenged by known data quality issues, and are not directly focused on serving the needs of the metabolomics community. ChemSpider is an online resource for the chemistry community hosted by the Royal Society of Chemistry with the intention of linking together online chemistry resources, cleaning and curating chemistry related data and collectively serving a number of communities. ChemSpider has been used by members of the mass spectrometry community, including instrument vendors, for the past 3 years. This roundtable meeting is to provide an overview of how ChemSpider is presently used by scientists working in the domain of metabolomics and garner feedback from the existing user base as well as new potential users to help define how ChemSpider can be enhanced to further support the needs of this community.

Antony Williams, VP of Strategic Development and host of ChemSpider at RSC, and John Shockcor, Director of Life Sciences Business Development at Waters Corp, invite you to attend thismeeting to provide input to steer development of ChemSpider to address the needs of the metabolomics community. An agenda will be defined in the near future based on interest.

If you are interested in attending please express your interest by sending an email to williamsa@rsc.org

 

The Royal Society of Chemistry will be heading to California for the Spring ACS Meeting where Antony Williams, the VP of Strategic Development for ChemSpider will be presenting several papers and hosting a ChemSpider Training Session.

The Training Session – “ChemSpider: A Community Resource for Chemical Data”  will be held on  Wednesday, March 30th from  8:30-11:00 AM in the Anaheim Convention Center,  Room 211 A.

This should be a lively and interactive session and is your opportunity to give feedback regarding present functionality and how you would like to see ChemSpider develop in the future. These sessions have proved popular in the past, so make sure to register early for your place here.

The titles and locations of the talks are:

RSC ChemSpider as an environment for teaching and sharing chemistry – Division of Chemical Education. March 28, 2011 from 9:45 am to 10:05 am. Disney’s Grand Californian Hotel , Room: Trillium B

Hosting a compound centric community resource for chemistry data – CINF: Division of Chemical Information. March 28, 2011 from 3:05 pm to 3:30 pm. Anaheim Convention Center , Room: 204 A

How the web has weaved a web of interlinked chemistry data – CINF: Division of Chemical Information. March 29, 2011 from 3:00 pm to 3:40 pm. Anaheim Convention Center , Room: 204 A

For a more pesonalized demonstration of ChemSpider you can also visit the RSC at Booth 903.

We look forward to meeting you in Anaheim.

On Monday 31 January, ChemSpider and Waters partnered with Chemistry World to deliver its first international live webinar and active audience event at Burlington House, London - Connecting Chemistry & Mass Spectrometry on the Internet.

Dr Antony Williams (RSC, ChemSpider) and Dr John Shockcor (Waters)  presented a top class and engaging event.

You can view the event by registering here:

http://chemistryworld.gav.co.uk/webcasts/event-detail/5/identification-of-metabolite-structures-using-mass-spectrometry.html

Earlier in the day we also hosted a round-table discussion for scientists interested in further refining how ChemSpider can be extended to serve the metabolomics community. Our thanks go out to all those who attended for a lively discussion.

We would be interested to hear your views -  for example, are there any additional features that you would like to have available or any other data sources that we should  link to?

GGA Software Services and Royal Society of Chemistry’s ChemSpider Announce Partnership

Cambridge, MA – January 28, 2011 – GGA Software Services, a leading provider of scientific informatics services to the life sciences and related industries, and Royal Society of Chemistry’s ChemSpider, a leading provider of chemical services and data on the internet, announced today a strategic technology partnership that will provide significant benefits to users of the ChemSpider chemical database.  The agreement makes available GGA’s open source Bingo chemistry search engine for use on the ChemSpider website, enhancing the ability of users of the ChemSpider service to efficiently conduct searches of the nearly 25 million chemical structures within the ChemSpider chemical database.

Bingo is a RDBMS data cartridge that provides the next-generation, fast, scalable, and efficient storage and searching solution for chemical information.  Bingo sets the industry standard in structure and reaction registration and retrieval, implementing state-of-the-art indexing algorithms within an underlying database server and making chemical searching fast and reliable.  Its extensible indexing enables scientists to store, index, and search chemical moieties alongside numbers and text within one underlying relational database server.  Users can seamlessly combine chemical substructure, reaction, and exact structure searching with numeric and text SQL terms.  It also has features not present in other cartridges — for example, advanced tautomer search, resonance substructure search, and fast updating of the index when adding new structures.

Richard Golob, President and CEO of GGA Software Services, states “We are very pleased to offer GGA’s Bingo search engine to users of the ChemSpider service.  As a professional services company, GGA would like to partner and share with others in the scientific informatics community to develop best-of-class open-source solutions.  Bingo, our open-source offering that is the result of five years of internal development, provides all the necessary search features required by chemoinformatics applications.  With Bingo, we have succeeded in achieving superior performance in a data cartridge for various types of searches, especially substructure search.  Users of Bingo will enjoy unsurpassed search capability for molecules and reactions.”

Antony Williams, Vice President of Strategic Development for ChemSpider, adds “ChemSpider has become one of the primary internet resources for scientists to search for chemicals and related information. The ability to efficiently search across a database of almost 25 million structures is a significant challenge.  We chose GGA’s Bingo offering as a result of the superior responsiveness of the GGA development team and the fact that the software is open source, thereby allowing us to extend the platform as necessary.  We look forward to a long and productive relationship with GGA Software Services.”

About GGA Software Services LLC

GGA Software Services is a leading provider of outsourced scientific informatics services to the life sciences industry.  Headquartered in Cambridge, Massachusetts, with a best-of-class development center in St. Petersburg, Russia, GGA offers broad capabilities in scientific software engineering, algorithm development, and knowledge, especially in cheminformatics and bioinformatics.  Global pharmaceutical, scientific instrumentation, and medical device corporations as well as early-stage life science companies rely on GGA to provide ongoing scientific informatics services, including support, maintenance, and QA services, to enhance their internal resources.  Since 1994, GGA has successfully served as an extended workbench for its clients, allowing them to both achieve their critical objectives and maximize their scientific informatics budget.  For more information, please visit our website at www.ggasoftware.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

Contacts:

Richard Golob

GGA Software Services LLC

One Mifflin Place

Cambridge, MA 02138

Tel: 617-491-5100

Fax: 617-491-0932

Email: info@ggasoftware.com

www.ggasoftware.com

Antony Williams

ChemSpider, Royal Society of Chemistry

904 Tamaras Circle

Wake Forest, NC 27587

Tel: 919-201-1516

Email: info@chemspider.com

www.chemspider.com

In response to your recent feedback we have now made it easier to see at a glance the Systematic name or PhysChem Properties for a compound.

Here is an example of the new record layout for glucose:

  glucose1

 

Clicking on any of the hyperlinks in the central column will expand the information available. The Search Google Scholar link will enable you to expand a search into the scientific literature based on the approved names and synonyms in ChemSpider.

Searching Similar will bring a table of compounds which share the same skeleton, but may have variations in the stereochemistry. The results are displayed in a grid format. New visual icons are now available to help you select the relevant record. These icons will tell you if there is information from Wikipedia, or if spectra are available for that compound.

 glucose2

Clicking on the structure image or the ChemSpider ID will take you back to the record view for each individual compound.

Other icons will be indicative of specific stereochemistry or double bond geometry or if the compound is a charged species or if it an isotope.

 glucose5

   = no, of defined stereocenters

  glucose6

                                = double-bond geometry

    glucose7

                                  = charged species

  glucose9

                              = non-regular isotope

glucose8                                   = spectra

    glucose4

                                           = Wikipedia

Scrolling down the record view will still give lots more information about the compound such as commercial vendors, links to biological, toxicity and safety data, as well as links to RSC journals, books and databases.

We have also made it easier for you to keep the information from different info boxes by adding a print button. For example you can now print a spectrum of interest.

 glucose3

 

Don’t forget that you can also Add your comments, compounds, literature references and spectra to ChemSpider by clicking on the right hand hyperlinks at the top of the record view.

For adding anything but comments you need to be a registered and logged on user.

Please do continue to let us know what you think about these enhancements and if there is anything else that you would like to see on the website.

Connecting chemistry and mass spectrometry on the internet in the very first Chemistry World live webinar on 31 January, discover the powerful combination of the modern mass spectrometry and the ChemSpider database of chemical structures in metabolomics research.

Dr Antony Williams of the RSC and Dr John Shockcor from Waters will be speaking on:

Connecting Chemistry and Mass Spectrometry on the Internet – ChemSpider
Monday 31 January 2011

Join the live webinar – Register Here

Or

Be part of the active audience at The Royal Society of Chemistry, London, UK – Register Here

This Chemistry World webinar is brought to you in partnership with ChemSpider and Waters.

I’ll shortly be announcing the details of a seminar we will be holding at the end of January regarding Metabolomics and ChemSpider. The details will come shortly. However, to parallel that seminar I want to be proactive in announcing that we will be holding a round-table discussion for scientists interested in further refining how ChemSpider can be extended to serve the metabolomics community. An outline of the meeting is provided below. If you are interested in participating please respond to me directly at williams”AT”rsc”DOT”org by the deadline listed below. We will cap the attendance fairly quickly and are specifically looking for people who can be vocal about their needs and how we may be able to help with ChemSpider as a platform.

Metabolomics Round Table – Delivering Value to the Metabolomics Community via ChemSpider, a Public Domain Database

Hosts: John Shockcor, Waters and Antony Williams, Royal Society of Chemistry

When: January 31st, 2011

Venue: Fish Room, Royal Society of Chemistry, Burlington House, London

The metabolomics community presently utilizes public domain databases such as KEGG, LipidMap, DrugBank and a myriad of other online resources to assist in the analysis of data. However, rich as these resources are, they are limited in scope, are challenged by known data quality issues, and are not directly focused on serving the needs of the metabolomics community. ChemSpider is an online resource for the chemistry community hosted by the Royal Society of Chemistry with the intention of linking together online chemistry resources, cleaning and curating chemistry related data and collectively serving a number of communities. ChemSpider has been used by members of the mass spectrometry community, including instrument vendors, for the past 3 years. This roundtable meeting is to provide an overview of how ChemSpider is presently used by scientists working in the domain of metabolomics and garner feedback from the existing user base as well as new potential users to help define how ChemSpider can be enhanced to further support the needs of this community.

Antony Williams, VP of Strategic Development and host of ChemSpider at RSC, and John Shockcor, Director of Life Sciences Business Development at Waters Corp, invite you to attend this half day meeting to provide input to steer development of ChemSpider to address the needs of the metabolomics community. This meeting will be followed by a public seminar and networking meeting in the RSC’s new Chemistry Center. An outline of the agenda is given below.

If you are interested in attending please express your interest by sending an email to williamsa@rsc.org by January 21st, 2011

12 – 1pm Arrival, Buffet Lunch

1-1:15pm Logistics and Intros

1:15-1:30pm An introduction to ChemSpider, Antony Williams

1:30-2:00pm Integrating ChemSpider and Metabolomics workflows, John Shockcor

2:00-4:00pm Round table discussion – How can ChemSpider expand to support the metabolomics community?

4:00-4:45pm Prioritization process

4:45-5:00pm Summary and Close

5:00-6:00pm Break

6:30pm Public Seminar

By now most of you are through the holiday season and recovering from the expenditures, both expected and unexpected, through the late nights and the joy of spending time with friends and family alike. The New Year provides a great time to reflect on the past year and think about what is coming in the year ahead…and making plans. For ChemSpider it has been a good year. Our reputation has continued to expand, our user base has increased, our staffing has increased and our participation in some major projects both within RSC and with international efforts for managing data have expanded. We won three awards, we recommitted to quality above quantity and we have worked hard to build a team of cheminformatics experts and programmers who can continue the charge to revolutionize the integration and delivery of chemistry-related data.

With this team in place we are set to make a lot of changes and enhancements in the coming year. This will be the year of deprecation. We have been busily flagging “bad” data…obvious errors that have found their way into the database. These will be dealt with, both in our database as well in other databases where we have migrated some of these erroneous data. A usability study has been conducted and the data are being analyzed and reviewed. An action plan to implement the appropriate changes based on this user feedback will be put in place early in 2011. This will be the year of RDF’ing ChemSpider…a certain community has been waiting for us to get this in place. We are committed to delivering it. We already started integrating the RSC Publishing Platform with ChemSpider through compound pages…a project to perform text-mining across the RSC article archive and link to ChemSpider will be initiated in 2011. Our much discussed “ChemSpider Education” project is underway and led by Martin Walker from SUNY Potsdam. The first view will be exposed at the ACS meeting in Spring. ChemSPider Synthetic Pages will continue to expand with new content and we are already busy assembling hundreds of spectra to deposit onto ChemSpider. We should be able to add another 1000 spectra in the next few weeks.

2011 is going to be an exciting year for ChemSpider…we hope you visit, give us feedback and challenge us to be our best. We are out to serve you, our community of users.

I recently talked about ChemSpider and some of our recent and future developments at the STM Innovations Seminar 2010, in a flash session of 20-slide talks timed @ 15 secs a slide. Great fun to do, and a format which ensures much less suffering for the audience – or at least shorter but more concentrated suffering. Anyway, here’s ChemSpider in 5 minutes for an audience of non-chemists. The other slides and videos from the Seminar are also available. Thanks to STM for hosting the event and River Valley for filming it.

The new content delivery platform from RSC Publishing provides powerful, fast access to journals, books and databases. You can search across nearly one million articles using one simple interface and refine your results through intuitive filters.

With the latest release a  new Compounds tab now displays the key chemical compounds from a journal article when it has been semantically enriched via RSC’s Project Prospect. Each compound links back to ChemSpider to access its 400 chemical data sources for compounds and users can also find related RSC journal articles containing the same compound.

 Phenylglyinol

 

Try it now by clicking on the ‘Compounds’ tab in the article - Total synthesis of (±)-Vertine with Z-selective RCM as a key step, Laetitia Chausset-Boissarie, Roman Àrvai, Graham R. Cumming, Céline Besnard and E. Peter Kündig, Chem. Commun., 2010, 46, 6264.

Effectively, you can run a text search within the Publishing Platform, perhaps by searching for your research topic or favourite author, to identify new papers and view the properties for any compounds in the article within ChemSpider.

Hi…ChemSpiderman (Antony Williams) here..I am about to start traveling and I will be giving a presentation next week in the UK. I have been working on some validation of online public domain chemistry databases. In doing this work I realized that what would be of benefit would be to hear from the community what databases you feel can be trusted and to what level. Please visit the online survey and provide me your feedback. This would be very useful for my presentation. If you could do this in the next 48 hours I would be very grateful. Thanks!

Click here to take my survey!!!

A recurring question which has come though our customer usability survey is “Can you copy and paste structures drawn in ChemDraw into ChemSpider?” The answer is yes, you can.  Simply draw the structure as normal and from the Edit menu choose Select All and  Copy. In ChemSpider choose Structure Search from the search menu and click on the structure image to activate one of the Java-based structure drawing applets.

  

 Structure image (3)

 

 

From the options given choose Draw/Edit and paste your structure into the drawing window, followed by Accept. You are now in a position to search your structure.

 

 Structure image (2)

 

 

Alternatively, rather than using this route you can save your structure drawing in ChemDraw as a .mol file and in the structure drawing applet of ChemSpider, select the option to Load, then navigate to the location of your saved .mol file, open and load.

 

 Structure image (1)

 


The ChemSpider web services are intended to allow you to use the functionality of ChemSpider and query the data in it in your own website or program or script. There are many different webservices as described here, and also many different ways to use them.

One example of how to use them was sent to us by Jimmy Moore from the University of Manchester. He includes a call on the SimpleSearch operation of the Search web service in a perl script. THis searches the whole of ChemSpider by an input value which can be the molecule’s name, SMILES string, InChI, InChIKey, and returns the ChemSpider ID:

use strict;
my $unknown = shift;
use SOAP::Lite on_action => sub {sprintf '"%s%s"', @_};
my $token = ' '; # Your token value should be input here. I'm not going to give mine away!
my $service = SOAP::Lite -> uri('http://www.chemspider.com/')
-> proxy('http://www.chemspider.com/Search.asmx');
my $output = $service->call(SOAP::Data->name('SimpleSearch')
-> attr({xmlns => 'http://www.chemspider.com/'})
=> SOAP::Data->name('query')->value($unknown)->type('')
=> SOAP::Data->name('token')->value($token)->type(''));
my @result = $output->valueof('//SimpleSearchResult/int');
print @result;

For further background, and also an example of a perl script which uses the SMILESToInChI operation of the InChI web service see his blog page.

Please note that to use this (and some of the other) web services you need to obtain a token, by registering with ChemSpider (if you have not already), and then logging into ChemSpider and viewing your Profile page. The Security Token shown needs to be copied into the perl script itself in Jimmy’s example.

Also note that you will need to install the SOAP::Lite for Perl modules to your Perl library to run this script if you don’t already.

If you have an example of how you have used the ChemSpider web services then please reply to this ChemSpider forum post. More examples will inspire more new ideas, and also make it easier for other people trying to do similar things.

Are you looking for bioactivity information for small molecules? ChemSpider now provides a direct link to the ChEMBL database from the European Bioinformatics Institute (EBI).

For example, take a look at the record for Fluconazole, an anti-fungal drug, in ChemSpider. If you go to the Associated Data Sources box and select Biological Data you will find the following links:

ChEMBL1

 

 

Clicking on the External ID link associated with ChEMBL will take you to the ChEMBL record.

ChEMBL2

 

 

 

 

The EBI produce both ChEBI (Chemical Entities of Biological Interest) and ChEMBL, a database of approximately 500,000 bioactive compounds. The bioactivities listed are abstracted from the scientific literature and are linked directly to the article.

You could also start your search in ChEMBL and then link back to ChemSpider to find additional information using the Std. InChIKey displayed in the ChEMBL record.

We like to make things easy for our users.

We hope you’ve had an opportunity to take a look at the revamped website. If you would like to share your thoughts on usability and design or site performance please take a moment to click on the “Give Feedback” button on the website. This will really help us to make the ChemSpider user experience even better.

 Kampyle feedback

ALPSP Publishing Innovation award 2010

Some of the team were present at the ALPSP Conference last Thursday – as the envelope was opened to announce ChemSpider as the winner of the ALPSP Publishing Innovation award for 2010! The judging panel commented that “[ChemSpider] has quickly become a highly valued and comprehensive community resource and has immense potential for future development”.

We’re especially proud as we were up against the other excellent shortlisted finalists of DataSalon’s Mastervision (which was highly commended, and we use it ourselves), the Semantic Biochemical Journal from Portland Press and the University of Manchester, and the AIP’s UniPHY social networking site.

We also managed to recreate the prize giving with Antony & Valery this morning – difficult to recreate the atmosphere of a conference dinner at 9am on an autumn Monday morning though…

Pics after the jump

Read the rest of this entry »

My presentation today at the Wolfram Data Summit in Washington DC gave me a chance to rant about the quality of data online and ask the question who really cares? Many of the database hosts don’t appear to care (most don’t respond to emails when I find errors, very few give anyway to annotate an error for example). The talk seemed to be well received and shocked a few people.

For all you Tweeters out there following Science Online the Twitter account for Aileen and Dave at the RSC  is  ChemSpider.

Not to be confused with that of Antony Williams who is still vey much ChemSpiderman.

Nature, Mendeley, and the British Library are excited to present Science Online London 2010. How is the web changing the way we conduct, communicate, share, and evaluate research? How can we employ these trends for the greater good? This September, a brilliant group of scientists, bloggers, web entrepreneurs, and publishers will be meeting for two days to address these very questions.

ChemSpider will be there to hear and record what is being said. If you are going to be there look out for David Sharpe and Aileen Day.

We will of course report back on topics that pertain to ChemSpider and the greater world of chemistry publishing.

Recently I co-authored a publication with Harry Pence for the Journal of Chemical Education. And today the news that it is published online. Please follow the instructions below if you want to be one of the first 50 people to obtain a copy.

“Your article, ChemSpider: An Online Chemical Information Resource, is now available on the Journal of Chemical Education website.  To view your article, please click on the ACS Articles on Request link below:

http://pubs.acs.org/articlesonrequest/AOR-gUuatr3ABq9RiePFMyaK

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