ChemSpider Blog

I want to acknowledge the support of one of our sponsors. For the past year or so we have had the following image on our home page. It’s pretty clear what this is for – molecular models. Very soon after we went live with ChemSpider Stephan Logan of Indigo Instruments and I chatted about what our intention with ChemSpider was in terms of providing a community resource for details about chemistry. Stephan offered his full support to us and I’ve enjoyed all of our discussions since then. I thank him and indigo Instruments for their support and, if you ever want a molecular modeling kit for your hands instead of your computer screen I recommend contacting them! An example structure for Xanax, in one of its flavors, is shown below. We’re looking forward to very “integrated” relationship with Indigo Instruments in the near future. Watch this space…

Jean-Claude Bradley from Drexel University has garnered the support of a number of high profile organizations to conduct an Open Notebook Chemistry challenge. Quoting from the Wiki “The first round of this challenge calls upon groups or individuals with access to materials and equipment to measure the solubility of compounds (aldehydes, amines and carboxylic acids are a priority) in organic solvents and report their findings using Open Notebook Science“.

I’ve been asked to participate as one of the judges on the panel. I must say that I am impressed by the quality of information being captured on the ONS wiki. We will be adding the outcome of the work to measure non-aqueous solubility measurements to ChemSpider.

The Journal of Visual Experiments (JoVE) is “an online research journal employing visualization to increase reproducibility and transparency in biological sciences.” Recently, one of our collaborators (and one of my friends) Jean-Claude Bradley from Drexel University was “published” to the JoVE journal with an article entitled “Optimization of the Ugi Reaction Using Parallel Synthesis and Automated Liquid Handling“. ChemSpider has been hosting some of the UsefulChem data as discussed elsewhere on this blog and it’s great to watch J.C and his students continue to get exposure for their work in this new way. He is certainly leading the path forward for Open Notebook Science.

I announced in July of this year that we were performing predictions using the EPISuite of prediction tools.I’m glad to say that one of our servers is now in “cooling mode” after running red hot for over 4 months. We’ve been feeding all single component ChemSpider entities with Molecular Weight <500 (non-radicals). The results are now posted on ChemSpider under the EPISuite tab. We hope you find them of value and offer our thanks to the EPA for providing us access to the software.

Chemical structure drawing packages are an essential tool for chemists in this day and age. There are many free offerings from chemistry software vendors given to the community. Companies such as ChemAxon, ACD/Labs, Cambridgesoft and others give their structure drawing packages to the community (as well as many other tools for some companies). Now a new structure drawing package has entered the freeware offerings and this is likely going to stir up the community. Many chemists will remember MDL and their ISIS Draw offering. For the longest period of time ISIS Draw and Cambridgesoft ChemDraw were the “most accepted” drawing packages – publishers would accept molecular structures submitted only from these applications. Despite the growth in popularity of other applications these remained the preferred tools. In industry these two held the primary position. In my previous role as Chief Science Officer at ACD/Labs I was very happy about the fact that we offered the ACD/ChemSketch package to the community and it is still available and new versions released on an ongoing basis. It’s a great package and almost a million downloads have been given away.

Now however Symyx Draw is available for free for academic and personal use. “Symyx Technologies, Inc. (NASDAQ: SMMX) today announced that Symyx Draw 3.1, the chemical drawing application that replaces industry-leading ISIS/Draw, is now available for download at no charge for academic and non-commercial personal use (www.symyx.com/getdraw). Symyx Draw 3.1 enables scientists to draw and edit complex chemical structures and reactions with ease, facilitating the collaborative searching, viewing, registering, and archiving of scientific information. To support academic researchers, Symyx Draw 3.1 also offers exceptional publication-quality drawing capabilities for presentations, reports and scientific papers, as well as improved integration with the Microsoft® Office suite of software applications. ”

Symyx Draw is a great replacement for ISIS Draw. It offers capabilities not previously offered in ISIS Draw. In particular, in my own area of interest it INCLUDES the generation of IUPAC Names and conversion of chemical names to structures. I tested some quite complex structures converting in both directions. Name generation from complex structures was very good. Conversion of chemical names back to structures worked well but I could not see how to generate the stereocenters in the resulting structures.I like the ability to search for InChIKeys across the internet directly – good thinking (and of course the searches I did took me to ChemSpider in 90% of the cases…)

Symyx Draw is offered with a whole series of add-ins that will extend its already excellent capabilities.I won’t list them here but point you to the list online.

I’ve just scratched the surface in learning the software package but I’ll likely switch to it for the next month or so as I did with Google Chrome. Then I can find it’s limitations and advantages and add it to the mix.

Maybe they’ll consider providing an add-in to search ChemSpider directly as ACD/Labs did with their add-on (the add-on does need updating by ACD/Labs however).

Welcome Symyx Draw to the mix…it’s a great offering

Chemical names generated by chemists can suffer from quality issues. Systematic nomenclature is not easy and software can definitely help…read this paper for example. If systematic names are not correct then either name to structure conversion algorithms or dictionary look-ups may fail. As we work to provide document markup capability and linkage to chemical structures contained within chemistry documents we need to account for these issues with naming.

As an example, see this online publication where even the same name is inconsistent. See below…

AN_interface is now available to edit the name “under the text” and therefore allow it to be converted OR to link it directly to a chemical on ChemSpider. In this way we are not adulterating the original text but now an “incorrect name” or name that is not associated with a structure for display is now available.

The input is easy…click edit in the structure balloon and then either edit the name or link to a CSID. Also, through this dialog you can declare it as a primary compound, secondary or catalyst. We can of course change this/add to this to be reactant, product, solvent etc.

Following the association/correction in this way the CORRECTed name shows up in the Balloon and the resulting structure is shown (and matches what’s in the article). One more step to optimal document markup.

We are adding additional dictionaries to ChemMantis to support linking to external information. Wikipedia is a rich source of information for chemists and we have chosen to connect out to Wikipedia for details about named reactions. Now, when a person marks up a document and highlights a particular named reaction then the link to Wikipedia is used to populate the information balloon on the article. An example is shown on this article on ChemMantis and the balloon is shown below for the Knoevenagel condensation.

As we work on ChemMantis it is clear that we want to expand the integration out to external sources of information as much as possible rather than limit the connectivities to the ChemSpider platform. We have started to build the necessary dictionaries to support bacteria, fungi, viruses etc so it makes sense to connect these up to external resources. As a proof of concept we are using Wikipedia sources to directly feed the “Species Balloons” and have enabled searching of Wikipedia, Google and Entrex directly from the balloon. As an example of the integration we see below the species balloon filled with the leed of the article from Wikipedia for Zymomonas mobilis(click on the thumbnail)

From the balloon it is possible to search across Entrez, Google and directly into Wikipedia for more information. For this particular bacterium Entrez gives a list of results as shown below (click on the thumbnail). We are using a similar approach with elements now. Rather than show a “bare element” in a structure balloon (who needs to see Li for Lithium?) we will display the leed text from Wikipedia for that element. The near future will likely see us link to Uniprot and PDB for proteins and out to similar rich sources for other species.

All reports about ChemMantis that I have reported to date have emphasized that ChemMantis only works in Internet Explorer. However, thanks to a comment from Soaring Bear, a member of our Advisory Group, I’m now looking at documents marked up with ChemMantis using the “IE Tab Add-on“. Details can be found here.This is an interim solution until we have direct support in Firefox.

We are progressing quite well with our development of Chemmantis, the document markup system for Chemistry-related documents. One of the problems with marking up various types of chemical entity is how “colorful” they can become as you markup a document. Some examples of markup we are considering are shown in the image. Not all of the supporting dictionaries are in place yet but are under development.

If you consider a standard chemistry document with the number of chemicals, reactions, elements and groups that can show up in just a paragraph you can end up with the “Christmas Tree effect”. An example of the effect is shown below. There are actually only three colors/effects shown – mark up of chemical names, mark up of elements and mark up of chemical names with no associated structure…in this case Bis-pi-allylnickel.

So, all elements are marked separately and, using the check box capability in the floating window, can be switched on and off. believe me, you need this. The words carbon, oxygen, nitrogen and hydrogen, for example, show clearly will up a lot in chemistry articles (hydrogen bond, carbon-carbon bond etc). So, there are many cases where you would just want to switch the element view off. One check box and its done. the same is true for chemical names, species and, shortly, chemical groups and reaction types. We are also working on splitting out bacteria, fungi, viruses etc.

If you want to see where we are at present I encourage you to look at this IUPAC Pure and Applied Chemistry article entitled : Carbon-Carbon Bond Forming Reactions Using Alkyl Fluorides. The markup does not yet work in any browser other than Internet Explorer so try it there. Hover over the chemical names and you should see the chemical balloon show up as shown below. In the next few days we hope to roll out the connections out to related data from this structure balloon. Watch this space.

I’ve posted a new presentation regarding ChemSpider/ChemMantis on Slideshare. The first part is the usual ChemSpider intro stuff. For ChemMantis start at slide 39…

Note that we’ve now started expanding the handling of “Species” handling by adding specific dictionaries. We’ll be adding support for fungi, bacteria, viruses etc. See slide 75 for a screenshot.

The ChemSpider Forum is starting to be used by users to resource information from the ChemSpider community. Not everyone reads the forum so i am trying to help the person who posted this request by exposing it to the readers of this blog in case you can help…

Looking for a surfactant

I own a small business, Superior Marker Company, and we make a unique type of blue chalk that’s used to mark the Bible, Blueprints and some Textbooks. The chalk erases from the paper, without harming it or leaving a permanent mark. Necessary to our process is a surfactant listed above, with two CAS Numbers, namely 68649-05-8 and 12676-21-0. One trade name for this product is “Armeen Z”, but it is no longer manufactured by Akzo Nobel. I’m scouring the globe for this product so if anyone knows where it can be found or if someone can synthesize it

Please visit the forum and respond if you can help: http://forum.chemspider.com/Default.aspx?g=posts&t=151

I previously posted a YouTube video of ChemMantis, our chemistry document markup system in action.While it is indicative of how the system works the detail is lost in the resolution of the video and there have been a number of requests for a higher resolution version. I’ve created a copy of the movie in Quicktime format and it can be downloaded from Mediafire here.

All feedback welcomed…

For those of you performing curation activities on ChemSpider you will likely have noticed the ability to mark a new type of identifier, a shorthand formula. We have enabled this because it has become clear that this could be a useful part of document markup as part of our ChemMantis system. For example, looking at an article let’s consider the excerpt shown below.

Regarding the excerpt you can see a number of highlighted terms, all being shorthand formulae and not depending on name to structure conversion algorithms but rather depending on a lookup dictionary. Each of these names are linked to ChemSpider for direct look up of information associated with the chemicals. The list of shorthand formulae extracted from a couple of hundred articles is actually only a couple of hundred formulae at present. It includes the most obvious compounds that we can all interpret: CH3OH, MeOH, CH3CN, MeCN, CH3COOH, NaCl, NaF, NaCN, KBr, KCl and so on. All of these are immediately interpretable by chemists. There are likely a few more to be found over the coming months but in the past week of reviewing articles from various sources we have actually only added a couple of new formulae. We have also seen value in linking up ions and elements as appropriate. We are likely to add filters for display/not display of elements and ions since we’re of the opinion that displaying every incidence of an element in an article is of luttle value…just imagine how many times you might see the word carbon or hydrogen in an article… carbon-carbon bonds, hydrogen bonding etc. So, we’re switching them off by default. We’ll keep reporting on how we are improving ChemMantis…based on the review of a stack of articles the system has improved dramatically. We are asking for your articles now…combining shorthand formulae and chemical name markup will highlight a document as shown below.