FAQs for ChemSpider

The ChemSpider service has been online since March 24th 2007 but we allowed beta-testers access to the system in January 2007. The FAQs below reflect on some of the most common questions they asked as well as some of the questions that we are expecting to be asked. If you have a question for us please send us your comments to our general inquiries email address at ChemSpider Feedback.

ALL ABOUT CHEMSPIDER

What is ChemSpider?

ChemSpider is a chemistry search engine. It has been built with the intention of aggregating and indexing chemical structures and their associated information into a single searchable repository and make it available to everybody, at no charge. ChemSpider is a value-added offering of publicly available chemical structures since many additional properties have been added to each of the chemical structures. We intend ChemSpider to offer the fastest chemical structure searches available online and delivered with the flexibility and usability necessary to encourage repeat usage.

Why did you name this service ChemSpider?

Anybody setting up a website with an intention of garnering traffic will tell you that a memorable moniker for the website does help. The ChemSpider domain name contains labels connecting the Chemistry nature of the website with the future “spidering” aspects of the site – connecting across the web to bring together disparate chemistry-related resources.

What is the ChemSpider logo based on?

ChemSpider™The ChemSpider logo represents the chemical structure of (1Z,3Z,5Z,7Z)-1,2,3,4,5,6,7,8-octaethylcycloocta-1,3,5,7-tetraene on a web-based background. It represents our ability to perform chemical structure searches across the world wide web.

  

Why are you providing this service for free?

ChemSpider is provided as a public service. The possibility to index and search all publicly available chemical structures via a website was originally conceived by our team about 5 years ago. At that time there were many technology hurdles, little time and no commercial reasons to pursue the project. Since that time technologies have matured and this project is presently undertaken as a hobby project with the intention of pushing the technologies and having an impact on the chemistry community at large. This project is presently self-funded.

Will this service stay free also in the future?

At present there is no intention to turn ChemSpider into a “for-charge” service. While we may seek sponsorship or advertising revenues in the future our present focus is on improving our technologies and developing a following for ChemSpider.

Is ChemSpider the first application of its kind?

ChemSpider is a software technology utilized to perform structure and text-based queries of a very large dataset of millions of chemical structures and associated data. ChemSpider is not the first application to allow this.

In terms of the gold standard in curated data CAS remains the premier offering. The CAS registry is the largest current database of chemical substance information in the world and contains more than 30 million organic and inorganic substances and 58 million sequences. You are referred to the CAS website should you be unaware of the CAS registry and services delivered by the organization. The need for this reference is, of course, unlikely.

The PubChem database provides information on the biological activities of small molecules and is a component of NIH's Molecular Libraries Roadmap Initiative. The Pubchem database presently contains close to 6 million compounds and is the result of combining data from a group of contributors.

eMolecules provides an indexing and search service to help find information about chemicals on web sites across the world wide web. eMolecules delivers chemical data aggregated by searching the internet, and from submissions from data providers such as chemical suppliers and academic researchers.

While ChemSpider is not the first application to allow free access to search a database it does offer a series of unique capabilities. The database is the largest online database available at the time of writing (over 10 million compounds). The system offers the greatest flexibility in structure based searching including exact structure, substructure and soon will include similarity of structure including matching stereochemistry and isotopes. These capabilities are enabled utilizing a structure drawing applet. ChemSpider also offers access to a series of calculation services utilizing a transaction based system.

Is ChemSpider selling a software package ?

ChemSpider is a web-based application delivering access to a database of publicly available chemical structures enhanced with related data generated by a series of prediction engines. Neither ChemSpider nor the associated database are part of a software package and will not be made available for sale.

BEHIND THE WEB OF CHEMSPIDER

A) Database Content

Where are you sourcing your content databases?

Our database is built up from an aggregate of data sourced from a series of publicly available data sources and from our collaborators. The list of data providers is available online. This list will continue to expand and will be updated on a regular basis. ChemSpider also has the ability to accept data submitted by our users. In this way we are offering the opportunity to develop an Open Chemistry Community of users.

I have collected set of structures of and want to make this available via ChemSpider. How do I do it?

The ChemSpider website offers to any chemists the ability to add to the database content. In order to submit the data through the clearance process simply use the outlined process and forms.

B) Online Services

Why are some of the properties not calculated for some of my molecules?

The algorithms utilized at the online services page are provided by third parties. All algorithms have specific limitations and predictions cannot be performed in all cases. We apologize for this and welcome your feedback when you identify issues with the online services. We cannot guarantee any resolution.

Please explain how the Simple Search Screen works for text searching?

The simple search screen allows searching based on Systematic Name, Synonym, Trade Name, SMILES string or InChI string. The search works by first searching on the synonym. if nothing is found then it converts the synonym to an InChI string if possible (using ACD/Labs Name to Structure conversion software). If nothing is found using the InChI as the basis of the search then a search is performed using the originally input text to search as a substring of a synonym.

How good are your logP value calculations relative to others?

The logP calculations performed online at ChemSpider are performed using a number of different logP predictors. ACD/Labs, one of the algorithm providers, have reported a number of comparisons of performance themselves and there have been a series of reviews reporting similar comparisons.

Why do you only allow fairly simple molecules as inputs to your nomenclature generation program?

The online transaction server utilized to generate the standardized nomenclature is described at the ACD/Labs website. The Free Naming is limited to molecules containing no more than 50 atoms, and no more than 3 rings, with atoms from among only H, C, N, P, O, S, F, Cl, Br, I, Li, Na, and K.  

Which other interactive services do you plan to install at your site ?
At present we do not have any other services awaiting installation. If you have services that you would like to suggest that we integrate with, or have your own services that you would like to connect into ChemSpider please contact us at feedbackATchemspiderDOTcom.

C) The Computing Behind ChemSpider

Will the users have access to the source code or ChemSpider database?

While ChemSpider is provided as a public service it is not an Open Source development. Neither the source code nor the aggregate database will be made available for download. Individual molecules or small hit lists can be downloaded from the database. Certain predicted properties may be excluded from the download.

What programming language(s) are you using?

ChemSpider is developed using a series of components and programming languages. Its core is written as highly optimized C/C++. The database engine is Microsoft SQL Server and the Web user interface is programmed using state of the art ASP.NET and C#. Various server-side scripting is done in Perl.

What is the software and hardware platforms?

ChemSpider is hosted on a x86 server-class PC running Windows 2003 Server

 

RIGHTS TO USE

Am I allowed to use the data I find on ChemSpider in a publication ?

Yes, all data displayed onscreen at ChemSpider can be used in a publication.

May I use your service in my teaching class ?

Absolutely. We would especially like the academic community to benefit from the information available on ChemSpider.

May I download the data and use it in my own database(s)?

You have limited rights in this regard. You can only assemble a database of 5000 structures or less, and their associated properties, from our database without our permission. You can download up to 1000 structures per day from the website. Please contact us at feedbackATchemspiderDOTcom to request an extension outside this constraint. We are willing to provide the ENTIRE database of ChemSpider structures at your request - the file will consist of InChI Strings, InChIKeys and ChemSpider IDs. These constraints are under regular review so please feel free to engage us in conversation.

  

  

CHEMICAL STRUCTURE REPRESENTATION AND SEARCH ENGINE

Why does the structure drawing applet load very quickly the second time I use the ChemSpider website?

The Structure Drawing Applet (SDA) is cached the first time you use the website and applet. Provided that you do not clear the cache the SDA will load very quickly for subsequent searches.

  

Why isn’t the ChemDraw Plug-in supported yet?

This is simply a matter of time, effort and requests. Should our user base determine that the SDA is insufficient to support their needs and request support for other structure drawing editors we will consider adding support for other applications. Please send your requests to feedbackATchemspiderDOTcom.

  

Can I perform chemical structure and substructure searches directly from the SDA applet?

Yes, substructure searches can be performed directly from the SDA applet. Please refer to the SDA manual for how to draw the appropriate substructures for searching.

Our company policy does not allow Java. How can I input molecules for searching into ChemSpider?

ChemSpider has been integrated to ACD/ChemSketch PC-based software, both the ChemSketch Freeware and the Commercial ChemSketch versions. ACD/ChemSketch can be run on Macintosh and Linux systems under an appropriate emulator.

You allow submission of SMILES, InChI strings and InChIKeys for structure searching. What are SMILES and InChI?

SMILES is a simple yet comprehensive chemical language in which molecules and reactions can be specified using ASCII characters representing atom and bond symbols. A SMILES string is human readable, is very compact, and if canonicalized produces a unique string that can be used as a universal identifier for a specific chemical structure. For further details the reader is referenced to the excellent tutorial on the Daylight website.

The IUPAC International Chemical Identifier (InChI) is a non-proprietary identifier for chemical substances. It was developed in a collaboration between IUPAC and NIST with the intention of enabling easier linking of diverse data compilations. The InChI source code and application programming interface is made available at no charge to the public. The reader is referred to the project pages for ongoing status reports.

  

PROVIDING FEEDBACK TO CHEMSPIDER

How do I report bugs to ChemSpider developers?

Please send all bug reports at bugs@chemspider.com. We will do our utmost to respond to you quickly but please note that registered users do receive preferred treatment.

How do I submit new feature requests for the ChemSpider service?

Please send all new feature requests to feedback@chemspider.com. We will do our utmost to respond to you quickly but please note that registered users do receive preferred treatment. Our receipt of new feature requests is no indication of our commitment to include your request in our future developments.