CLiDE – making chemical information a lot more accessible
As scientists we all learn to cope with ever growing amounts of information, coming from various sources. Scientific information, as virtually all types of information, is predominantly delivered in electronic formats – journal articles, patents, e-books, wiki pages, blogs, etc. We need this information to be readily accessible, and searchable, we archive it on our personal PCs, and on our organization’s servers and knowledge bases. As chemists, we have wonderful visualization techniques that allow us to sift through incredible amount of data, and information, but exactly in this place, there is a strong disconnect between the availability of information and its accessibility. 2D images of molecules are so pivotal to the way we digest chemistry, and yet, as images they are not too prone to our data mining tools. It would be great if publishers of chemistry articles were to retain the original structures in their electronic documents and there is no doubt that this will happen some time in the future. But, for now, we need a tool which can translate chemistry images into a connection table format which could allow integration of data from the literature into existing chemistry software.
CLiDE is an optical chemical structure recognition engine. It extracts connection tables of molecules from 2D images in various formats: PDF, postscript, JPEG, BMP, PNG, and TIFF. CLiDE has been around for some time now, but in the last two years it finally got the development boost it deserved, in order to make it a cool and useful instrument for every chemist’s toolkit. It is now equipped with a sleek GUI that can be used to read .pdf as well as a variety of image file formats. Any time you come across a structure of interest, simply select it, extract it, and save it, or send it to your favourite chemical editor (currently ChemDraw, ISISDraw and SymyxDraw are supported). We all know the feeling of looking at a page full of structures that are relevant to our work, and would like to transfer them to another application such as an Excel spreadsheet or a docking program but redrawing them using a graphic editor is tedious and prone to mistakes. CLiDE takes away this hassle. It comes in three flavours that can either process a single image at a time (standard), a whole document at a time (professional), or a full library of documents in one go (batch).
Below you’ll find a demo clip of the new CLiDE product, please contact us to obtain a password to watch it.
March 8th, 2010 at 8:38 pm
The latest CLiDE v3.0 version’s interface looks quite improved and much easier to use … Thanks, and great job!