FAIR Data Hackathon / BioAssay Express

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 […]

KNIME integration with BioAssay Express

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 […]

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, […]

BioAssay Express: crowd curation now technically possible

Until earlier this week, the public facing instance of the BioAssay Express was basically read only: we carried out our curation exercises by passing files around. As of now, though, it is possible to authenticate yourself using ORCID and submit your annotations. From that point your changes will be stored in a special holding bay until they are approved. This […]

BioAssay Express: models mixing assays & compounds

The latest experimental feature of the BioAssay Express project involves taking all of the curated assays (3500 so far) and their corresponding compounds from PubChem (hundreds of thousands of unique structures) and feeding them all into one giant Bayesian model. Rather than the usual approach of modelling compound ⟹ activity separately for each assay, this approach takes advantage […]