Re: NeuroLex questions

[Stephen Larson]

Hi Rick,

  Good questions.  Comments below:

On Mon, Mar 3, 2014 at 3:15 PM, Rick Gerkin <rge...@gmail.com> wrote:

Stephen,  

I've been getting NeuroLex IDs from Open Source Brain projects (http://opensourcebrain.org/projects.json) and programatically generating validation tests from NeuroElectro data via its API and the NeuronUnit testing framework I've been developing.  

One issue is that some NeuroLex IDs are not represented in NeuroElectro, but seemingly identical neurons with different NeuroLex IDs are.  For example:  

sao2128417084 vs. nifext_50

Both of these appear to be layer 5 pyramidal neurons.  The former is initially defined more broadly, but in the defining criteria it says that the soma is located in layer 5, as with the latter

http://neurolex.org/wiki/Sao2128417084 had an erroneous defining criterion -- that has just been fixed.  It is intended to be the more general one, encapsulating all cortical pyramidal neurons, not just layer 5, like nifext_50 does.  Good catch.

Another case is:

nifext_52 vs nifext_53

Both of these appear to be layer 4 stellate cells.  

nifext_53 is pointing at a deleted page, so that ID should be dead.  nifext_52 is what you are looking for. 

Because NeuroLex is pretty flat, there doesn't seem to be much of a way of finding out that these are related neurons, or even the same neuron.  In the case that they are the same neuron, I'm not sure what the mechanism is for flagging this and getting the merged.  Let me know if there is anything I can do to better understand this or help clean it up.  

Basically each ID can be put into a URL to inspect the page itself as I did above.  This is the primary way to see what is going on with an ID.  You can check the history, see if the page has been deleted, see if the page is in good standing.  You can get an account and make edits yourself if you notice problems.

The list I've cc'ed here: neur...@googlegroups.com is a good mechanism for asking questions like this one if you are unsure about going in and making edits yourself.

Hope that helps -- let me know if there are more questions.

Best,

  Stephen

 

Rick