Re: Question about NeuroLex URI resolver for Neuron Types

[anita bandrowski]

Hi Shreejoy, Thank you for being a good uri using citizen!

I will check on this issue, but if the page exists then the resolver should work.

We have not changed the uri policy on NeuroLex, but a bug may have been introduced.

I am cc-ing the neurolex group just in case others are having the same problem and they have additional examples.
I poked around in the ones we use and they seem to work, but Zaid did create a bunch of neurolex redirects recently to solve some persistent redirect issues so this may be a side effect.

Best,
anita

On Mon, Feb 17, 2014 at 9:54 AM, Shreejoy Tripathy <stri...@chibi.ubc.ca> wrote:

Hi Stephen and Anita,

I've been linking out to neuron types in NeuroLex from NeuroElectro (like a good neuroinformatics resource builder!) using the neurolex URI resolver: e.g., http://uri.neuinfo.org/nif/nifstd/sao830368389

This works great from some neuron types, but for others (like those whose definitions have since changed over the past couple years), like these:

Neocortex Martinotti Cells : http://uri.neuinfo.org/nif/nifstd/nifext_55

and

Thalamus Relay Cells : http://uri.neuinfo.org/nif/nifstd/nlx_cell_20081203

I get a series of either redirect pages or pages to deleted neurons. However, these neurons still seem to exist (via their id's) in NeuroLex (e.g., http://neurolex.org/wiki/Category:Neocortex_Martinotti_cell)

Do you guys know what's going on? Is this an issue with the URI resolver? Should I be using a different tool for this?

Let me know if I can expect an answer on this soon, I'm currently working on reviewer responses and want to get this figured out asap.

Thanks,

Shreejoy

--

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

[anita bandrowski]

Hey Shreejoy,

For that example, it looks like the redirect from neurolex.org/wiki/nifext_55 was broken. I updated it to the new name and it now works fine, including the uri.

Our bot should do this at the point of page save, but perhaps it does not over-write existing pages?

Zaid can you clarify the behavior of the save page bot:

We know that when you create a page in NeuroLex with some id, then a redirect and URI is created for some id.

If a redirect page exists already (as in this case where the page was renamed), does it over-write the existing one or does it not?

     - If not, then we should potentially update the behavior to over-write old redirects.

     - If so, then we should probably run your save page bot to update the broken links.

On Mon, Feb 17, 2014 at 11:30 PM, Shreejoy Tripathy <stri...@chibi.ubc.ca> wrote:

Hi Zaid,

Thanks for checking this out. I'm a bit confused about what the default behavior should be.

To me, it seems like if I hit the URI service with a neurolex id, then it should directly return me the page with the matching neurolex id. For example, if I use the link: http://uri.neuinfo.org/nif/nifstd/nifext_55, then it should resolve to the following page directly: http://neurolex.org/wiki/Category:Neocortex_Martinotti_cell, because the latter is the only page with the the id nifext_55. Am I missing something here?

Best,

Shreejoy Tripathy
University of British Columbia
Post-doctoral Researcher
Centre for High-Throughput Biology

On Mon, Feb 17, 2014 at 11:11 PM, Zaid Aziz <zaida...@yahoo.com> wrote:

Hi Shreejoy,

First of all, I want to thank you for reporting the problem. I checked the examples your provided in the email, and it seems that those Neurolex page were deleted by Neurolex users. Deleting a page does not delete its redirect page. I believe that the URI resolver is working fine. Do you face this problem frequently? If your answer is yes, or you need more help with the issue please don't hesitate to contact me so we can figure out something around this problem.

Best,

Zaid 

[Shreejoy Tripathy]

Hi Zaid,

Thanks for checking this out. I'm a bit confused about what the default behavior should be.

To me, it seems like if I hit the URI service with a neurolex id, then it should directly return me the page with the matching neurolex id. For example, if I use the link: http://uri.neuinfo.org/nif/nifstd/nifext_55, then it should resolve to the following page directly: http://neurolex.org/wiki/Category:Neocortex_Martinotti_cell, because the latter is the only page with the the id nifext_55. Am I missing something here?

Best,

Shreejoy Tripathy
University of British Columbia
Post-doctoral Researcher
Centre for High-Throughput Biology

On Mon, Feb 17, 2014 at 11:11 PM, Zaid Aziz <zaida...@yahoo.com> wrote:

Hi Shreejoy,

First of all, I want to thank you for reporting the problem. I checked the examples your provided in the email, and it seems that those Neurolex page were deleted by Neurolex users. Deleting a page does not delete its redirect page. I believe that the URI resolver is working fine. Do you face this problem frequently? If your answer is yes, or you need more help with the issue please don't hesitate to contact me so we can figure out something around this problem.

Best,

Zaid 

On Monday, February 17, 2014 10:52 AM, anita bandrowski <aband...@ucsd.edu> wrote:

[Shreejoy Tripathy]

Hi Anita and Zaid,

Thanks for checking on this for me!

Would it be too much trouble to have a bot check on the URIs for the rest of the NeuroLex Vertebrate Neurons : http://neurolex.org/wiki/Vertebrate_Neuron_overview?

Best,

Shreejoy Tripathy
University of British Columbia
Post-doctoral Researcher
Centre for High-Throughput Biology

[anita bandrowski]

Will do.

Zaid just wrote some code to fix the resource branch, so this should be straightforward.

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