The Learn Chemistry Wiki also goes a step further and not only contains compound information in isolation but also contains laboratory experiments (with parallel sections which contain an overview, teachers’ notes and students’ handouts) for each, quizzes, and tutorials which are linked to the compound information to put them into context. The wiki is based on the MediaWiki platform (which allows multiple users to contribute collaboratively since the website is intended to be a community website), but extends it to incorporate functionality similar to that of ChemSpider, invoked via custom-made extensions. For example, it is possible to draw structures using GGA’s Ketcher in order to find structures, or to draw answers to quiz questions (for example to specify the product of a particular reaction). It is also possible to include an interactive spectrum retrieved from ChemSpider in any wiki page, using the ChemDoodle spectrum viewing widget in browsers which support canvases or JSpecView applet in those that don’t.

For an overview and demonstration of the Learn Chemistry Wiki site see the Learn Chemistry Wiki site tour webppage or the Learn Chemistry Wiki overview demo video:

The Learn Chemistry Wiki is part of the new RSC’s new Learn Chemistry platform which provides a central access point and search facility to make it easier to access the various different RSC teaching resources that it provides.

We have experimented with adding a node to a project which would call the ChemSpider webservices to perform a simple search on it and the instructions below outline how to reproduce our experimentation. This was done with KNIME 2.5.0, with the KNIME extension “Generic Webservice Client” installed.

1. From the Node Repository find the “Generic Webservice Client” under the “Misc” folder and drag it into the Knime project to add a new node
2. Right-click on this “Generic Webservice Client” and click on the “Configure…” option
3. The WSDL for each ChemSpider webservice can be found using the link from the page for the appropriate webservice. For example, the WSDL for the Search webservice is at http://www.chemspider.com/Search.asmx. However, if you enter this as the WSDL location you’ll get an error when you click the “Analyze” button (due to a SOAP exception “undefined simple or complext type ‘soapenc:Array’. This is something that we’re looking into addressing in ChemSpider, but for now a workaround is to copy the WSDL, replace the old fashioned soapenc:Array type with tns:ArrayOfString, and save and use this ammended WSDL locally. I have done this with the Search webservice and the resulting WSDL is available for download here. This file should be downloaded, adn extracted somwhere locally. It can then be entered in the “WSDL Location” field of the Generic Webservice client in KNIME (using a location of the form: file:/C:/temp/ChemSpiderSearchWSDL_no_soapencArray.WSDL) which will then be processed correctly on clicking the “Analyze” button
4. Set the Port, operation, inputs and outputs as required – see screencapture below for settings for my demonstration. Note that you should use your own token as the value for the token input – if you don’t have one already then see the instructions here for instructions.
5. Add input and output nodes which connect to and from this Generic WebService Client node as required. For example, you could add a FileReader node as the initial node, which reads in the contents of a text file that simply contains a search term as an input (and adapt the Input value accepted as the query input value of the SimpleSearch to map to this column, rather than hardcoding in a value to search for). And the output csid could be written to a csv file using a CSV Writer node.
6. On executing the workflow, an output csv file is created which contains the ChemSpider ID(s) of any compounds that match the search term. In the case of a search for “benzene” the csid retrieved is 236.

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 Steven 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.

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.

1. Search by name – systematic name, synonym, trade name
2. Search by chemical identifier – InChI, InChIKey, SMILES
3. Search by database identifier – registry number

4. Search by exact structure drawn, substructure, similarity – exact match, all tautomers, same skeleton (including/excluding H), all isomers
5. Draw an exact structure – in one of several structure drawers

6. Load from mol, sdf, skc, cdx files
7. Load from an image of the structure – gif, png, jpg, tiff – to get an editable/correctable structure for search

8. Convert an identifier or name to a structure, to use or amend in the structure search

9. Search for compound with/without a particular element or elements
10. Search by properties – molecular formula, mol wt, nominal mass, average mass, monoisotopic mass. Exact match or within a range
11. Search by calculated properties range – ACD/LogP, ACD/LogD (pH 5.5), ACD/LogD (pH 7.4), Rule Of 5, Number of Hydrogen Bond Acceptors, Number of Hydrogen Bond Donors, Number of Freely Rotatable Bonds, Polar Surface Area, Polar Surface Area, Molar Volume, Refractive Index, Boiling Point, Flash Point, Density, Surface Tension
12. Search by data sources – select one or many individual data sources (from the 400 we hold), one or many data source types from Available Chemicals Databases, Biological Properties , Chemical Reactions, Chemical Safety Data , Drugs or Compounds in Development, Imaging Agents , Information Aggregators, Journal Publishers via MeSH , Ligand/binding/crystal Structure Databases, Metabolic Pathways , Molecular Libraries Screening Center Network, Natural Products, NIH Substance Repository, Patents, Personal Collections, Physical Properties (including SAR/QSAR databases), Protein 3D Structures, Publication or Magazine Article, Spectroscopy Databases , Substance Vendors, Theoretical Properties, Toxicology/Environmental Databases, Virtual Library, Web-based Article (blog or commentary)
13. Search by focussed library – Building Blocks, Screening Compounds, Building Stock, D-EXP014, Acetylcholinesterase (AChE), cAMP dependent protein kinase (PKA), Estrogen Receptor (Alpha), Phospholipase A2 (PLA(2)), Test Set for DILI modelling, Test Set for DILI modelling, Training Set for DILI modelling
14. Search by ligand screening – LASSO (Ligand Activity in Surface Similarity Order) similarity
15. Combine search to look for Single- or multi-component structures
16. Combine search to look for, or disregard, isotopically labelled structures
17. Filter results with analytical data

18. Use our web services for mass spectrometry to search by molecular mass or elemental composition within ChemSpider or within particular data sources,
19. Use our web services to search by chemical identifier, retrieve information about ChemSpider record, retrieve the chemical structure thumbnail
20. Use our web services for spectra to return all Open Data spectral information from ChemSpider, return spectral information on a compound, return identified spectra
21. You can show all spectra of a particular type on the spectra page

What have we done?

We’ve regenerated all of the InChIs in the database with version 1.03 of the InChI code.

What does that mean?

The InChI (international chemical identifier) is a short piece of text that describes the structure of a molecule. Each one is generated by a free and open-source computer program, which guarantees that it should be the same and there shouldn’t be conflicting InChIs for the same molecule. You can’t really write them by hand, because they look like this:

InChI=1S/C10H22ClN2O5PS/c1-3-10(9-18-20(2,15)16)12-19(14)13(7-5-11)6-4-8-17-19/h10,12H,3-9H2,1-2H3

ChemSpider is built on InChIs. If two molecules have the same InChI, then they’re the same record in ChemSpider, and if you can’t InChIfy it, you can’t put it in ChemSpider. That’s why we can’t do, for example, polymers yet.

We’re proud to be founder members of the InChI Trust, which supports this critical element in the sharing of chemical compound information.

What does all this mean for ChemSpider?

Because there is an active community supporting InChI who look out for these things, version 1.03 contained some bug fixes which mean that a very small number of the InChIs themselves, only a few dozen out of the whole database, have changed.

• P⁺–O^– bonds and P⁺–S^– are now treated slightly differently. This means that it will be easier to find the exact molecule you’re looking for, regardless of how it’s been drawn. (In principle this will also apply to analogous bonds containing arsenic, selenium, tellurium and antimony, but I can’t see any examples of this in the database.)
• There was a small bug where the InChI generated for a molecule with an azide group in it sometimes varied according to the input drawing. But that doesn’t happen now.

This regeneration has also allowed us to catch and clean up some errors in the data.

What happens next?

Version 1.04 of the InChI code will be released soon. With our new framework for processing large amounts of data we’ll be able to update our InChIs much quicker. The main changes in 1.04 that affect the InChI are to how it handles radical atoms in aromatic rings, nobelium, lawrencium and rutherfordium, so we anticipate that there shouldn’t be very many changed InChIs!

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”

ChemSpider is a free chemical structure database providing fast access to over 25 million structures, properties and associated information. By integrating and linking compounds from more than 400 data sources, ChemSpider enables researchers to discover the most comprehensive view of freely available chemical data from a single online search. For more information, please visit www.chemspider.com

The Southampton work builds on work from the RC-UK & EPSRC funded e-Science CombeChem and Platform projects (GR/67729, EP/C008863, EP/G026238, EP/F05811X) and JISC Data Management projects.

About RSC Publishing
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 the University of Southampton
The University of Southampton is a leading UK teaching and research institution with a global reputation for leading-edge research and scholarship across a wide range of subjects in engineering, science, social sciences, health and humanities.

UoS Chemistry
The University of Southampton is one of the best places in the UK for teaching and research programmes in Chemistry. The research covers a broad range – from synthesis of novel molecules and materials to in-depth studies of chemical reactions and processes, and the modelling of chemical systems. There is a strong emphasis on interdisciplinary collaboration, and we support other institutions across the UK by providing unique services such as national X-ray crystallography service. www.soton.ac.uk/chemistry.

The oreChem Project
The oreChem project integrates Chemistry Scholarship with the Semantic Web (http://research.microsoft.com/en-us/projects/orechem/) involving groups from the Universities of Southampton, Cornell, Cambridge, Penn State and Indiana with funding from Microsoft Research (MSR)

About Microsoft Research
Founded in 1991, Microsoft Research is dedicated to conducting both basic and applied research in computer science and software engineering. Researchers focus on more than 55 areas of computing and collaborate with leading academic, government and industry researchers to advance the state of the art. Microsoft Research has expanded over the years to eight locations worldwide and a number of collaborative projects that bring together the best minds in computer science to advance a research agenda based on their unique talents and interests. Microsoft Research collaborates openly with colleges and universities worldwide to enhance the teaching and learning experience, inspire technological innovation, and broadly advance the field of computer science. More information can be found at http://www.research.microsoft.com

About Microsoft
Founded in 1975, Microsoft (Nasdaq “MSFT”) is the worldwide leader in software, services and solutions that help people and businesses realize their full potential.

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

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.

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.

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.

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

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!