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 michelle

Michael Dorf mdorf at stanford.edu
Fri Sep 1 15:27:59 PDT 2017


Hi Michelle,

Thank you for reporting this to us. Unfortunately, this is a known issue with the BioPortal backend parsing mechanism that is unable to correctly identify and mark root classes in SKOS ontologies. This issue is tracked here:

https://github.com/ncbo/ontologies_linked_data/issues/82

and here:

https://github.com/ncbo/bioportal-project/issues/36

The reason you are seeing search results from this ontology in CEDAR is that this bug specifically affects the root classes endpoint:

http://data.bioontology.org/ontologies/FAST-EVENT-SKOS/classes/roots (returns an empty set)

All other endpoints for the ontology, including the search, are functional:

http://data.bioontology.org/search?q=new%20deal&ontologies=FAST-EVENT-SKOS

We’ll try to prioritize fixing this issue in a timely manner. Please, check the Github links above for the latest status of our progress.

Thank you,

Michael


On Aug 31, 2017, at 2:19 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: michelle

Email: futo at stanford.edu<mailto:futo at stanford.edu>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2F

Feedback:

submitted FAST-EVENT-SKOS which per its publisher is a SKOS file (http://experimental.worldcat.org/fast/). It has over 15,000 individuals. When I go to Classes tab in BioPortal, I get "problem retrieving classes". When I use FAST-EVENT-SKOS in CEDAR to constrain values of a field, I can search for terms. And when I populate the template, I see a dropdown of terms. But in both cases only about 20 terms (out of ~15,000) appear. I've shared the CEDAR template, called "test", with CEDAR dev team group

_______________________________________________
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/20170901/ce05687b/attachment.html>


More information about the bioontology-support mailing list