NeuroLex Namespace and Programmatically Accessing Terms

[Nolan Nichols]

I'm curious what the best way to reference a term on Neurolex is. Recently a whole bunch of DICOM terms were added to NeuroLex (thanks for than btw!), and I am wondering about how to reference their URI's.

Say I want to reference "TE", which is located here: http://neurolex.org/wiki/Category:Echo_Time

And it has the NeuroLex ID of "nlx_149938"...

My question is, what is the base namespace URI for neurolex ID's, such that I would be able to dereference them? Is this possible?

I'm thinking something like this:

prefix: neurolex: "http://neurolex.org/term#"
neurolex: nlx_149938

Where  "http://neurolex.org/term#nlx_149938" would either take me to http://neurolex.org/wiki/Category:Echo_Time or an RDF representation of the term.

Thanks! Hope that made sense.

Cheers,

Nolan

[Stephen Larson]

Easy: http://neurolex.org/wiki/nlx_149938

That will get you the webpage.

For RDF:  http://neurolex.org/wiki/Special:ExportRDF/nlx_149938 

Here's some python code you could use to grab the graph using rdflib:

import rdflib
#Get a Graph object
g = rdflib.Graph()
# pull in an RDF document from NeuroLex, parse, and store.
result = g.parse("http://neurolex.org/wiki/Special:ExportRDF/nlx_149938", format="application/rdf+xml")
print ("graph has %s statements." % len(g))

Cheers,

  Stephen

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[Maryann Martone]

There is a structure for Neurolex URI's.  I've cc'd Jeff and Anita so they can give it to you.  But we should expose the full URI on the Neurolex page.  The next question is a harder one.  We generally like to keep the source URI's or identifiers so as to avoid having to do extensive mapping.  We recognize, however, that as a term is exposed in Neurolex, it may be modified in a way not intended by the source.  We have toyed with the idea of fixing a set of metadata from the source so that it cannot be modified, but I am against that, as I think it's counter to the spirit of the wiki and also doesn't allow for corrections to be easily made or value added to a term that is specific for the neuroscience community.  So there are a few options:

1)  Use the Neurolex ID;  maintain a mapping to the source ID, as we do currently with DICOM
2)  Use the Neurolex ID in Neurolex, but use the source ID in NIFSTD, as NIFSTD tends to use direct imports;  maintain the mapping to Neurolex in NIFSTD
3)  Use a hybrid URI, with the prefix indicating its current home:  http://neurolex and its suffix indicating the source  http://neurolex/DICOM:204,472.

On Wed, Sep 5, 2012 at 3:52 PM, Nolan Nichols <nolan....@gmail.com> wrote:

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[Nolan Nichols]

Thanks for your response, Maryann.

  So there are a few options:

1)  Use the Neurolex ID;  maintain a mapping to the source ID, as we do currently with DICOM
2)  Use the Neurolex ID in Neurolex, but use the source ID in NIFSTD, as NIFSTD tends to use direct imports;  maintain the mapping to Neurolex in NIFSTD
3)  Use a hybrid URI, with the prefix indicating its current home:  http://neurolex and its suffix indicating the source  http://neurolex/DICOM:204,472.

Perhaps a good topic for discussion this week in Munich?

Cheers,

Nolan

[Jessica Turner]

Well it wasn't clear to me what the implications of these choices were, or why one might be better than another under different situations, so if there's a discussion of it let me know. :)

Thanks,

Jess

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Jessica Turner, Ph.D.
Associate Professor, Translational Neuroscience

Director of Operations, 3T MRI Center
Mind Research Network
1101 Yale Blvd. NE
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email: jtu...@mrn.org

[Maryann Martone]

In the sense of a URI, I don't suppose the syntax really matters, as it is technically supposed to be meaningless.  But for bookkeeping and attribution purposes, I have been thinking that #3 makes the most sense.  It recognizes the source of the concept, without the need to maintain a separate mapping.  It should be easy to parse the specific ID part so that we can use it as a point of aggregation.  At the same time, it says that this is not coming from DICOM but from Neurolex and Neurolex will modify it and use it as it wishes. 

So, we are going to declare our URI structure once and for all, and put it on all pages.  We will all meet in Munich and decide on the structure and that will be that!