Some time ago I described a Safari extension that uses the chemicalize.org to index a web page for chemical content.
For an example of a “chemicalized” page have a look at this
As you can see below all molecules mentioned in the page become links that on a mouse over reveal the structure, they also provide a handy ribbon of structures across the top of the page that is useful for quickly scanning and navigation.
A recent publication by Southan and Stracz, Extracting and connecting chemical structures from text sources using chemicalize.org. Journal of Cheminformatics 2013, 5:20 describes how this information is being used to provide better indexing of the internet in a chemically intelligent manner. They include a demonstration of a number of web pages and document sources that were indexed in this manner including PDF’s from the patent office.
chemicalize.org now has 15000 unique visitors a month – which is a huge growth compared to spring 2012. These users contribute to the database every day, making sure it’s up-to-date and contains new interests as well. The database today contains 327000 structures that were converted from 545000 names and identifiers coming from 367000 webpages.
These structures and links have now been uploaded to PubChem and if you are interested in what sort of molecules have been registered via chemicalize.org you can browse them on the PubChem website here
When Apple released Safari version 5 one of the most important new features was the support for extensions. Extensions are a great way to add features to Safari to personalise web browsing, they enable the addition of features that you find useful. There is a listing of Extensions that might be useful for chemists and judging by the weblogs these are of significant interest. If you are working with them however it is a bit of a pain to check which are installed and which are enabled. This applescript is a very neat way of getting a report, it also serves as a demonstration of how to link to shell scripts, in particular using the unix command
cat, a standard Unix utility that concatenates and lists files, to generate the report.
Just updated the chemistry Safari extensions so they are compatible with the upcoming Safari 5.2.
There are a number Safari Extensions described on this site that access similar services and with the help of Matt I'm happy to anounce a new addition.
The Safari Extension for Opsin (download) allows the user to highlight a chemical name in a web page and then control click affords a dropdown menu, click on "Display ... using Opsin" and a small window will open displaying the chemical structure. What is particularly nice is that in addition to providing the structure in png format the same web service also provides the chemical structure in SMILES, InChi and CML format. If you click one of the buttons and the bottom of the structure window the structure will be downloaded in the appropriate format. You can read more about this extension here.
There is a full listing of the Safari Extensions here.
The structure is displayed in a larger window as shown below. Clicking the “Save” button downloads the structure in .mol format.
Back to list of extensions
A selection of extensions that should be useful for chemists.
Chemspider :- Displays structure of highlighted chemical/drug and links to ChemSpider page.
PubChem :- Search PubChem for the highlighted compound
eMolecules :- Search eMolecules for the highlighted compound
Chemicalize :- Submit the current URL to chemicalize.org
DrugBank :- Search DrugBank for the highlighted compound