Multiple Neurolex pages for GO terms

[Trish Whetzel]

Hi Stephen,

Can you explain the difference between the pages (1) http://neurolex.org/wiki/Category:Cellular_component and (2) http://neurolex.org/wiki/GO_0005575?

Is page (2) intended to be deprecated following the update in the format of GO Ids?

Trish

[Maryann Martone]

Hi Trish:

I think Anita might have to explain that one.  Note that the GO ID terms are under the root "Wiki" and not "Category".  I believe that is the case with all our ID redirect pages, although I'm not sure why this decision was made.  So this will be a good discussion thread to find out.

Maryann

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[anita bandrowski]

Hi Trish,

The second page, you will notice is not a "real" wiki page.

This is the text that tells you "There is currently no text in this page. You can search for this page title in other pages, search the related logs, or edit this page."

The thing that happened here was the the redirect page was not created properly for this concept, so instead of the id redirecting to the entity, it actually just makes a call to ontoquest to see what ontoquest can tell us about this concept. We have this dependency on ontoquest because we did not have all entities in the wiki.

In cases like this, we can fix the (2) page by adding would work.

#REDIRECT [[:Category:Cellular component]]

I have not done this yet though because I looked at a bunch of other GO pages and they are not redirecting properly. Zaid just fixed a bug in the redirect generating code that should fix the redirect page generation when users touch terms and it looks like these pages were created when this was not working properly.

Basically the wiki would create redirects for nlx_ids but not foreign ids.

Let me do a bit of testing and try to figure out a fix.

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

[Trish Whetzel]

Thanks Anita and Maryann,

The issue with the wiki pages came up in discussion with Chris about updates of SAO Ids with GO Ids in the wiki. While there were a few signals that the page at: http://neurolex.org/wiki/GO_0005575 was not a typical ontology term page it's also not entirely obvious why this page exists. It sounds like resolving the page Redirects will fix this issue.

Another question, the link for the term name and ID displayed on the page at: http://neurolex.org/wiki/GO_0005575 points back to BioPortal using the old GO Id format and therefore does not resolve. Is the URI displayed on the wiki pulled from Ontoquest or is there wiki code that generates these links? I don't see the old formatted version of the GO URIs in the latest version of NIFSTD, however the production Ontoquest is a few versions behind the latest ontology release.

Trish

[anita bandrowski]

Hi Trish,

Sorry about my last email being somewhat incoherent. I added a ticket about this to the NeuroLex group. You are a watcher.

The old id format is something we need to resolve in OWL / Ontoquest.

Ontoquest holds all data that you see in the http://neurolex.org/wiki/GO_0005575 kinds of pages. The only thing that NeuroLex holds is the template of how to display it.

I will update some documentation in the NeuroLex to deal with these sorts of pages. People should know what they are looking at.

la Jolla, CA 92093-0608

[Trish Whetzel]

Hi Anita,

Yes, I saw the ticket. The email was clear, this was just a follow-up question to check if there were more issues that need to be resolved about how the URI for the term is generated in the wiki. The URIs in the OWL files and in Stage Ontoquest seem to be fine, so it's not clear why the links are generated as:
http://bioportal.bioontology.org/ontologies/GO?p=classes&conceptid=http%3A%2F%2Fpurl.org%2Fobo%2Fowl%2FGO%23GO_0005575, which fails to resolve

versus:
http://purl.obolibrary.org/obo/GO_0005575, which correctly resolves to OntoBee.

Trish

[anita bandrowski]

Hey Trish, I am not sure why we have the resolver going to the funky bioportal url.

Lets try to figure out if this is coming out of ontoquest or if this is a function of the "fake page" creation.

la Jolla, CA 92093-0608

[Trish Whetzel]

FWIW - Here is another example of a NeuroLex page that points back to BioPortal using a URL that does not resolve:
http://neurolex.org/wiki/PR_000013021

Trish

[Maryann Martone]

Is that because the URL is wrong on our end or did it change on Bioportal's end?

[Trish Whetzel]

Both, however Ontoquest contains the correct term URL so the mechanism that is generating the term URL used in NeuroLex needs to be identified and fixed.

Trish

[anita bandrowski]

Thanks Trish, I will alert Zaid so he can dive into this "fake page" code to see if that has a hard coded url someplace.

la Jolla, CA 92093-0608

[Trish Whetzel]

Great - thanks!  Let me know if there are any questions about what URL should be used. The preference is to use "obolibrary" PURLs for GO and PR and any other OBO Foundry ontology.

Trish

[anita bandrowski]

added you as a watcher.

la Jolla, CA 92093-0608