The last three weeks featured two meetings around data infrastructures for the NanoSafety Cluster. The first maating was on January 25-26 in Brussels, and last week the eNanoMapper project held its second year meeting with a subsequent workshop in Basel (see the program with links to course material). Here are some personal reflections on these meetings, and some source code updates based on the latter workshop particularly.
For the workshop in Basel I extended previous work on JavaScript and R client code for the eNanoMapper API (which I previously wrote about and see doi:10.3762/bjnano.6.165).
JavaScript
Nothing much changed for ambit.js (see these two posts) and I only added a method to search nanomaterials based on chemistry rather than names before (release 0.0.3 is pending). That is, given a compound URI, you can now list all substances with this URI, using the listForCompound() function:
var searcher = new Ambit.Substance(
“https://apps.ideaconsult.net/enanomapper”
);
var compound =
“https://apps.ideaconsult.net/enanomapper/compound/71/conformer/71“
searcher.listForCompound(compound, processList);
You may wonder how to get the URI used in this code. Indeed, one does rather than hardcode that, as it may be different in other eNanoMapper data warehouse instances. This is where another corner of the eNanoMapper API comes in, which is wrapped by the Compound.search() method. However, I have to play more with this method before I encourage you to use it. For example, this method returns a list of compound matching the search. So, how do we search for fullerene particles?
R package
The renm package for R was demonstrated in Basel too and some 25% in the audience uses R in their research. The README.md has some updated examples, including this one to list all nanomaterials from a PNAS paper (doi:10.1073/pnas.0802878105):
library(renm)
substances
service=”http://data.enanomapper.net/”,
search=”10.1073/pnas.0802878105″, type=”citation”
)
The 0.0.3 release made just in time of the workshop fixed a few minor issues. The above JavaScript …read more
Source:: r-bloggers.com
