Wednesday, June 4, 2014

Citations, DOIs, Pubmed IDs

Since we've started discussing the API for PyOpenWorm, we've started talking about putting up citations of data sources. What we're looking at doing is making a declarative API that allows us to write things like:

n1 = Neuron('AVAL')
n2 = Neuron('ADER')
r1 = n1.connectsWith(n2) # r1 is now a representation of this 'connectsWith' relationship
s = Chemical('X')
r2 = s.modulates(r) # r2 is the representation of the 'modulates' relationship
e = Evidence(doi="http://dx.doi.org/10.1007%2Fs00454-010-9273-0")
e.asserts(r2)

In English, "10.1007%2Fs00454-010-9273-0 suggests that chemical X modulates the connection between AVAL and ADER". This 'relationship' API (a sub-API to the PyOpenWorm API), has the primary feature of allowing statements made as to be part of higher order statements.

No comments:

Post a Comment