Missing connections in linked data representation

[Chris Mungall]

I'm exploring the linked data / RDF representation of neurolex, and am finding that certain paths that are traversible on the wiki are not traversible in the RDF, due to missing connections.

For example, it seems I should be able to go from Area29ofisthmusof_DMVH2003 to 'macaque', via a path link this:

Area29ofisthmusofDMVH2003 --subClassOf--> DMVH2003parcellationschemeparcel --XXX--> DMH2003parcellationscheme_parcel --Species--> Macaque

Unfortunately, the XXX link is missing. This appears to be something to do with aliased pages on the wiki where the aliasing is not present in the RDF.

On the wiki, these two pages have equivalent content:

[DMVH] http://neurolex.org/wiki/Category:DMVH2003_parcellation_scheme_parcel
[DMH] http://neurolex.org/wiki/Category:DMH2003_parcellation_scheme_parcel

One appears to be a redirect of the other.

In the RDF, these have the following URLs (note the URLs in the RDF are subtly different from the HTML which is a little unfortunate and confusing)

[DMVH] http://neurolex.org/wiki/Category-3ADMVH2003_parcellation_scheme_parcel
[DMH] http://neurolex.org/wiki/Category-3ADMH2003_parcellation_scheme_parcel

A number of RDF URIs connect to the DMVH one. However, this appears to be a dead end in the triplestore, it is not the subject of any triples. The DMH URI is the subject of some triples. However, there is nothing connecting the DMVH and DMH URIs. This means that data from the former is unconnected to data in the latter. For example, we cannot traverse this path:

Area_29_of_isthmus_of_DMVH2003 --subClassOf--> DMVH2003_parcellation_scheme_parcel --XXX--> DMH2003_parcellation_scheme_parcel --Species--> Macaque

Because there is nothing in the XXX position.

Is this a known limitation of the linked data representation of neurolex? What is the preferred form of programmatic / query access to neurolex?

[anita bandrowski]

Trish may have to weigh in on the path question, but I did notice that the redirect page code was not correct and that code creates subcategories when it is not correct. 

The redirect page on the DMH page http://neurolex.org/w/index.php?title=Category:DMH2003_parcellation_scheme_parcel&redirect=no

was 

#REDIRECT [[Category:DMVH2003 parcellation scheme parcel]]

I changed it to 

#REDIRECT [[:Category:DMVH2003 parcellation scheme parcel]]

This is subtle, but without the : before the category while creating a redirect, also creates a subcategory.

If this is fixed in the RDF in roughly an hour (after the next dump into virtuosso) then it means that this was the problem.

--
You received this message because you are subscribed to the Google Groups "neurolex" group.
To unsubscribe from this group and stop receiving emails from it, send an email to neurolex+u...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

--

Anita Bandrowski, Ph.D.
NIF Project Lead
UCSD 858-822-3629
http://neuinfo.org
http://orcid.org/0000-0002-5497-0243
9500 Gillman Dr.#0446
la Jolla, CA 92093-0608

[Trish Whetzel]

Chris, let me know if this is still an issue after the update to Virtuoso.

Trish

[Chris Mungall]

I downloaded the version withe creationDate 2014-07-23, and there is still a lack of a connection between the two

[Trish Whetzel]

OK, we'll look into this further.

Trish