CAS Registry Numbers in Properties Viewer
by Andras Stracz on January 3, 2012
Today we added a new structure identifier to the Properties Viewer: CAS Registry Numbers.
For those who are not yet familiar with CAS numbers, they are unique numerical identifiers assigned by the Chemical Abstracts Service to every chemical described in the open scientific literature. Check out the wikipedia article for a more detailed description.
Your input structure’s CAS number is resolved using the “cactus” nih.gov web service at: http://cactus.nci.nih.gov/
We hope you find this latest addition to chemicalize.org useful!
Update: Extending the datapage with QSPR / ADMET calculations
by Andras Stracz on December 8, 2011 • Tagged as: property calculation
Thanks for those who reacted to the earlier blog entry, your opinion is highly appreciated. However, it seems that there is not enough interest in QSPR / ADMET calculations, so we will not be working on it in the near future.
Leave your commentInstant Structure Extractor
by Andras Stracz on September 26, 2011 • Tagged as: document mining
chemicalize.org lets you view webpages or PDF documents with chemical structures highlighted, but what if all you have is a piece of text? On the chemicalize.org frontpage, you can now paste any text for instant structure extraction.
Here’s how it works: when you paste some text, we add 2 large text fields to the page (if it doesn’t look like URL or a chemical structure name and it’s longer than 1 average length English sentence).
The first text field, Original, will hold your input. The second, chemicalized, will show the highlighted version where you can mouse over the names to see the 2D structure image just like on a webpage. You can keep editing the original version, and the chemicalized version will automatically update.
That’s it, we hope you find this little feature useful! If you’d like to see improvements for this, please fill out this short survey!
2 commentsIntroducing the Document Viewer
by Andras Stracz on September 20, 2011 • Tagged as: document mining, PDF
Today we launched a new service on chemicalize.org (as we mentioned in previous blog post: Upcoming new feature – extract molecules from PDF files) to enable viewing and extracting chemical structures from PDF files.
Before any technical details, here’s a demo with an open access article: Simple isatin derivatives as free radical scavengers… Chen, 2011.
The Document Viewer – strongly resembling the existing webpage viewer – includes the following features:
- view PDF document in the browser
- find and highlight location of structures
- extract chemical structures from the document
Due to the nature of PDF files, access may be limited as follows:
- uploaded PDF – only you have access, others may only see the abstract
- link to PDF on the web – public, others will see the entire document
To get started, go to http://www.chemicalize.org/ and click upload.
This development was added based on your feedback, so we hope you’ll enjoy it! Don’t forget to let us know your thoughts in the short questionnaire below!
Leave your commentUpcoming new feature – extract molecules from PDF files
by Andras Stracz on August 29, 2011 • Tagged as: document mining, PDF
Update: Introducing the Document Viewer
Based on your feedback, we have started implementing a new service for chemicalize.org that will allow working with PDF files. Currently planned features include: displaying the PDF file, extracting the molecules found in the text. The images below will give you more ideas about our plans.
Thanks for everyone who contributed on the survey! If you are interested in the results of the short questionnaire you can see a summary of responses here.
Comments OffDeveloper presentation on chemical name to structure conversion
by Andras Stracz on August 29, 2011 • Tagged as: document mining
The archive of ChemAxon’s latest user group meeting recently opened with downloadable presentations and videos.
Among others Daniel Bonniot, the developer of ChemAxon’s and chemicalize.org’s naming tools, presented the latest news and changes in our technology. You might be interested in his presentation which is available in ChemAxon’s online library.
Leave your commentExtending the datapage with QSPR / ADMET calculations
by Andras Stracz on June 23, 2011 • Tagged as: property calculation
We are thinking about extending our property calculation datapage with Quantitative-Structure Activity Relationship (QSAR) and/or ADMET calculations.
We would like to collect the most popular and reliable state of the art approaches in the field providing an interface for the medicinal chemistry community where structural properties and their applications are available.
As an example, currently we are looking at the following equations from Current Medicinal Chemistry, 2006, 13, 2653-2667, Tingjun Hou et al:
- Blood-brain barrier penetration:
- Caco-2 apparent permeability coefficient:
Please help us with suggestions by filling the survey below or share your thoughts in the comments section!
3 commentsImplementing mobile interfaces
by Andras Stracz on May 30, 2011 • Tagged as: chemical search, document mining, property calculation
We are thinking about adding mobile interfaces to chemicalize.org so you can use chemicalize.org with your favorite smartphone or tablet.
Supported devices would include Android phones and tables, iPhones and iPads, Opera Mobile and Mini, Blackberry devices and many more.
Due to the limited screen size and different controls (i.e.: touch instead of mouse + keyboard) on these smartphones and tablets, we are planning a limited service – initially only chemicalizing webpages and calculating properties -, but we need your help to identify the important information on these pages.
Please help us finalize our plans with the survey below or share your thoughts in the comments section!
6 commentsExtending structure search with context
by Andras Stracz on May 30, 2011 • Tagged as: chemical search, text search
We are thinking about extending the chemical search service with this contextual search options. You could extend your structure search with other related structures (similar structures, substructures, superstructures, tautomers, etc…) and non-chemical text such as disease names or research areas.
Web search already provides a solution for this, but because it is powered by Google, searching with related structures is not possible. It can however search the entire internet, while our chemical search service is limited to our database.
To help with understanding how useful it would be, please help us with filling the survey below or share your thoughts in the comments!
5 commentschemicalize.org for MediaWiki
by Andras Stracz on May 30, 2011 • Tagged as: mediawiki, plugins
We are thinking about creating a plugin for Mediawiki (the content management system that powers wikipedia.org and most other wikis) that would allow chemicalizing wiki pages automatically. With this, selected pages of your wiki would get chemical structure recognition capabilities.
The features would very strongly follow the existing WordPress plugin: automatically process content when it’s being edited; displaying the processed version where recognized names are underlined and on mouseover displaying a tooltip with the 2D structure image of that structure.
Help us to find out how useful this is to you, please fill out the survey below or share your thoughts in the comments section!
2 comments