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.

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Recently I described an open source tool for editing chemical mixtures, using a machine readable format. Now we have a proof of concept tool for starting with the kinds of text descriptions people use to describe mixtures, and recreating the actual components in their full glory. Continue reading →

The Molecular Notebook desktop app for chemical structure & data content creation has gotten a refresh on the iTunes AppStore: it now responds to the dark-mode preference. 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 →

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 →