The BioAssay Express project captures a lot of public bioassay data using public ontologies, and quite often these ontologies overlap with each other: this happens particularly often with the target concept. We needed to map common terms between the Drug Target Ontology and Uniprot (via the Protein Ontology) with a mapping file. The amount of data involved was a […]
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 […]
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 […]
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, […]
It’s been awhile since I wrote a post. Most of my work these last few months has been on the BioAssay Express project, which has been advancing forward on every front: technology, data, collaborations, commercialisation, and even a software patent.
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 […]
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 […]
Since the BioAssay Express project added molecules to supplement the annotated assays, we have been able to explore various interesting visualisation techniques. One of the obvious options is to plot a table with assays on one axis and compounds on the other, and look for insights regarding which molecules light up the various different screens.
The BioAssay Express project has been moving forward at a solid pace: several important new features have been added or improved for locating assays and inspecting them, with an eye toward performing some sophisticated analysis and model building. This is motivated by the fact that we have curated quite a few assays (~3,500) which is sufficient […]
The last post described the addition of molecules to the BioAssay Express project, and alluded to the near term intention of making this actually useful for something. The first round of utility is now in place: the ability to select columns and download the molecules as a single SDfile, suitable for use as a structure-activity […]