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[bioontology-support] Partial index of search results for ontology

Michael Dorf mdorf at stanford.edu
Thu Aug 18 18:18:09 PDT 2016


Hi Simon,

I've looked into your submission, and there are definitely several components of the processing of GRID ontology that are questionable. When opening this ontology in Protege, it appears that most of the entities inside are individuals, with only 9 entities identified as "classes". Because our metrics calculation reports only 9 classes, our downstream processing (search being one of them) fails to index the entire contents of the ontology.

While Protege and our internal metrics data are consistent (9 classes and 63216 individuals), our classes endpoint appears to display the individuals as classes, so there seems to be an inconsistency in the way we treat this ontology's content:

http://data.bioontology.org/ontologies/GRID/classes/

Our parsing expert engineer is on vacation until next Monday. When she's back, we both will continue looking into this problem.

The good news is I was able to tweak our indexing code internally and re-index the GRID ontology in a way that would include all classes/individuals. The search that was previously failing now works:

http://data.bioontology.org/search?q=digital&ontologies=GRID

Hopefully this will allow you to complete your demo. I'll keep you posted on the rest of the issues.

Thanks!

Michael


On Aug 18, 2016, at 13:21, Simon Porter <s.porter at digital-science.com<mailto:s.porter at digital-science.com>> wrote:


Hi I'm having a problem with the autocomplete/search results of the portal

I have submitted an ontology: http://data.bioontology.org/ontologies/GRID<http://data.bioontology.org/ontologies/GRID/classes/http%3A%2F%2Fwww.grid.ac%2Finstitutes%2Fgrid.452594.b>

however, only some results are appearing in search results

the main problem I have is that only a small amount of classes are appearing in the search results.

for instance: http://data.bioontology.org/ontologies/GRID/classes/http%3A%2F%2Fwww.grid.ac%2Finstitutes%2Fgrid.452594.b exists

but it doesn't show up in the search  (widget example below), but it is also the case for the search api
<image.png>

any help appreciated!

Thanks,

Simon
--
Simon Porter
VP Academic Relations and Knowledge Architecture
Digital Science
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