New items on AppStore: XMDS and MedChem Toolkit

newappsIn the last couple of weeks, two new items appeared on the iTunes AppStore under the Molecular Materials Informatics account: the Medicinal Chemistry Toolkit and XMDS. Continue reading


BioAssay Express: converting annotations into prose

The BioAssay Express project is about describing bioassay protocols using machine readable annotations (which are URIs that have been appropriated from semantic web dictionaries). Because almost all currently existing bioassay protocols are represented as text, much of the focus has been on finding ways to streamline the annotation process. Thinking forward to the future, however, we anticipate that once this technology is widely deployed, scientists will find it easier to annotate new protocols using our templates and web-based interface than to write up many pages of prose using a wordprocessor.

For this reason, we are experimenting with running the process in reverse: converting the nicely structured semantic web annotations to scientific English, so that the biologist doesn’t have to do. Continue reading

American Chemical Society meeting: Fall 2017 Washington D.C.

bae_bayesiansThe autumn ACS meeting is coming up next month, and I will be presenting two talks:

  • Sunday (20/Aug) 10:30-10:55am: Presentation in Division of Chemical Information (Open Structures: Current Issues & Future Plans) – Representing molecules with minimalism: A solution to the entropy of informatics
  • Wednesday (23/Aug) 10:50am: Presentation in Division of Chemical Information (Drug Discovery: Cheminformatic Approaches) – Autonomous model building with a preponderance of well annotated assay protocols

Continue reading

XMDS with MolPress

xmds_molpress06Last week’s post mentioned the MolPress plugin for WordPress running on an actual website ( The purpose of the plugin is to add a convenient use case for incorporating chemical data into an article, and having it rendered as a diagram that’s just as good as a dedicated picture. This fusion of machine & human readable content is desperately lacking in the realm of chemical data communication of all kinds, from electronic lab notebooks to the peer-reviewed literature. Continue reading