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

American Chemical Society meeting: Spring 2017 San Francisco

ACS_BAEPoster_20170318I’m much looking forward to the impending meeting, which starts this weekend. For anyone who is going to be attending, I’ll be making an appearance in several preordained locations:

  • Sunday (2/Apr) 7-9pm: Poster in Division of Medicinal Chemistry, West Hall – Moscone Center: Bioassay protocols: Semantic annotation to enable informatics (see thumbnail)
  • Monday (3/Apr) 8:15am: Presentation in Division of Chemical Information, Metropolitan II – Park Central SF: Expanding the target dimension: How to visualize a lot of SAR
  • Friday (7/Apr) 10:15am: CDD special event, American Bookbinders Museum SF: Assay informatics with the BioAssay Express (BAE): when protocols are machine readable, good things happen

And as well, I will be found lurking around the Collaborative Drug Discovery booth (#1620) in the expo haul at key moments, particularly during the lunchtime rush.