Lately I’ve been working on a new extension to the InChI identifier which is intended to broaden its domain to include the universe of non-organic compounds and all of the insane diversity of exotic bonding types. Preliminary results of the first stage are up on GitHub. Continue reading
It’s been awhile since I’ve posted anything, but not for lack of activity in the world of sciencey-informatics. Next week I’ll be at the BioIT World FAIR Data Hackathon in Boston, along with several other members of the Research Informatics team of Collaborative Drug Discovery. Right now we’re tooling up a customised instance of the BioAssay Express (for which the most uptodate standard version can be found here) so that we can deploy several different proposed templates for evaluating whether a published article abides by FAIR principles. The plan is to evaluate as many articles as we can, and produce a scoresheet at the end of the day. I don’t know what the answer will be, and it will be interesting to find out!
One of the pitfalls of using multiple public ontologies is that sometimes there are two teams doing great work that overlaps, but neither is a superset of the other. This has come up for the BioAssay Express project, which uses both the Cell Line Ontology and BRENDA cells & tissues.Continue reading
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