Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] [BioPortal] Feedback from Maxwell Neal

Michael Dorf mdorf at stanford.edu
Wed May 18 14:49:08 PDT 2016


Hi Maxwell,

This should be resolved now. It looks like GO hasn't been indexed for a while, and the version we have in our search index is not the latest submission of the ontology. I've done some more granular troubleshooting of indexing this specific term:

http://purl.obolibrary.org/obo/GO_0005891 (voltage-gated calcium channel complex)

There is absolutely nothing abnormal about it. It indexes just fine in my local environment. Please let me know if you continue experiencing issues with this or see any other abnormalities with our search.

Thank you,

Michael


On May 11, 2016, at 12:16, Maxwell Neal <maxneal at gmail.com<mailto:maxneal at gmail.com>> wrote:

OK Michael thanks very much for the update!

M

On Wed, May 11, 2016 at 3:00 PM, Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>> wrote:
Hi Maxwell,

Thank you for bringing this to our attention. At this point, I don't have a definitive answer for you other than "it should work, but it doesn't". :-) One thing I did verify is that the term IS missing from our search index. Troubleshooting this further isn't trivial as it requires a "controlled" re-indexing of the ontology to see whether this term gets skipped, errors out, or simply returns empty data.

I'll have to get back to you oaths, hopefully within days.

Thank you for your patience!

Michael


On May 10, 2016, at 08:05, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Maxwell Neal

Email: mneal at uw.edu<mailto:mneal at uw.edu>

Location: http://bioportal.bioontology.org/ontologies/GO?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FGO_0005891

Feedback:

Hello,

I'm having trouble retrieving the GO term "voltage-gated calcium channel complex" (GO_0005891) using the BioPortal REST services. When I use the following call, no results are returned:

http://data.bioontology.org/search?q=voltage-gated+calcium+channel+complex&ontologies=GO&format=xml&exact_match=true&apikey=c4192e4b-88a8-4002-ad08-b4636c88df1a

Also, a broader search on "calcium" does not return the term:

http://data.bioontology.org/search?q=channel&ontologies=GO&format=xml&exact_match=false&apikey=c4192e4b-88a8-4002-ad08-b4636c88df1a

Any help is appreciated!

- Max

_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support



-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20160518/436dfac3/attachment.html>


More information about the bioontology-support mailing list