The ChEMBL-og

We have just had a paper accepted in PLoS Computational Biology on the work we've done on allosteric modulators (first mentioned on the blog  here ).  The work is based on the mining of allosteric bioactivity points from ChEMBL_14. The data set of allosteric and non-allosteric interactions is available on our FTP site ( here ). This blogpost will just highlight some sections of the paper, but we would like to refer the interested reader to the full paper ( here ).  Dataset The dataset contains ChEMBL annotated and cleaned data divided in both an 'allosteric' set and a 'non-allosteric' (or background) set. Abstracts and titles mentioning allosteric keywords were pulled and from the resulting papers we extracted the primary target and all bioactivities on this primary target. From the remainder of the papers we also retrieved the primary target and all bioactivities on this primary target in a similar manner.  Targets When we observed the target distr...

“ Pharmaceutical Knowledge Retrieval through Reasoning of chEMBL RDF ” is the title of my master thesis, a twenty-week research project performed at the Department of Pharmaceutical Bioscience at Uppsala University (Prof. Wikberg, supervised by Egon Willighagen ). The project aims at using the ChEMBL data with a technology that might be new to some: by using semantic web technologies. The life sciences workbench Bioclipse (doi: 10.1186/1471-2105-10-397 ) has support for several semantic web tools, including RDF , and was used to establish such a connection. Two aspects were looked at in this study. Firstly, we developed the search functionality for ChEMBL data to use RDF. For this, we took advantage of the RDF-ized ChEMBL knowledgebase (using the data from ChEMBL 02). Secondly, we developed a use case where compounds derived from ChEMBL are analyzed with the substructure mining software MoSS (see the Bioclipse Wiki ). Here, we search for common and discriminative substructures ...