Awhile back I described the idea of bond artifacts, which are layered on top of a core cheminformatics representation to give the rendering engine the hints it needs to make the visual diagram look like what chemists want to see (without breaking the underlying machine readability). Now this enhancement has been added to the open source WebMolKit framework and the derived SketchEl2 drawing app. Furthermore, the artifacts can survive a round trip encoding with the industry standard Molfile CTAB format. Continue reading →

At CDD we’ve recently begun a new project to define a common format for mixtures of chemicals, along with an open source editor, and impending tools for generating data from text content. The work-in-progress editor is now openly available on GitHub. Continue reading →

One of the things I’ve been investigating lately is the open access segment of PubMed, which is a rather massive collection of open access medicine-relevant publications, with accompanying full text.  Similarly with the ChEMBL database, which is focused on structure-activity data traceable back to the original literature document from which each datapoint was curated. This is all for the purpose of advancing the BioAssay Express mission of making the world’s bioassay protocols machine readable (aka FAIR). Continue reading →

As of now, there’s a KNIME plugin that can be used to access data from the BioAssay Express. The plugin uses the existing API functionality that can grab all of the available bioassay protocols, or a subset as defined by a query, and bring them into the KNIME ecosystem as a table which can be processed using the multitude of other node types. Continue reading →

ACS time is sneaking up on us, as it tends to do: in about 2 months from now – August 2018 – a large proportion of the world’s chemistry community will be converting in Boston, including myself. This particular city is probably my favourite venue, simply by virtue of being such a massive hub for various forms of chemistry and derived industries, such as small molecule drug discovery.

My presentation will be on the Wednesday:

As for the last couple of meetings, I will be presenting aspects of the BioAssay Express project, on behalf of Collaborative Drug Discovery. Our team has been quietly expanding in numbers and working hard making the product more powerful and more polished, so there are lots of new features to talk about!

The interactive sketcher feature in WebMolKit now has a more accessible demo page at molmatinf.com/webmolkit.html. Continue reading →

Last week I had the pleasure of representing Collaborative Drug Discovery at the BioIT World Hackathon, themed around FAIR data principles. Continue reading →