Saturday, December 07, 2013

Programming in the Life Sciences #14: Two more projects

Two more projects were handed in for Programming in the Life Sciences late last night (see also the first three). Roberto developed a web page where you can enter a search term after which it will search targets based on that term, count the number of pharmacological data, and when selecting a target, it will summarize the IC50 values, pCHEMBL values, and molecular weights, like in this screenshot:

Anniek and Darja had a really interesting idea: start with Alzheimer and find possible drug targets, and with the Open PHACTS 1.3 API that should be possible with, e.g. the Alzheimer pathway in WikiPathways. However, while they got Ensembl identifiers for the targets in the pathway, after struggling for half a day, they could not find any pharmacology data. It turned out that the mappings between the Ensembl and Uniprot IDs were not to be found in the 1.3 cache (which still is the case). So, in the end, I created a JSON identifier mapping data for them to look up the mappings in. They ended up visualizing the results in a HTML table, where the target names were dynamically added to the table's "Coding Protein" column, addressing the asynchronous calling of the Open PHACTS APIs: