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[bioontology-support] ECSO search via API

Ben Leinfelder leinfelder at nceas.ucsb.edu
Tue Sep 13 14:15:34 PDT 2016


Looks great and thank you!
-ben

> On Sep 13, 2016, at 1:26 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu> wrote:
> 
> Hello Ben,
> 
> The latest version of ECSO is fully available now.  Apologies for the delay - we had our ontology parsing process locked down briefly while we imported the 2016AA version of the UMLS.
> 
> Best,
> Jennifer
> 
> 
>> On Sep 13, 2016, at 10:03 AM, Ben Leinfelder <leinfelder at nceas.ucsb.edu> wrote:
>> 
>> Hi John,
>> It's me again :). I'm trying to be patient with the parsing and indexing queue for a new version of our ECSO ontology, but figured I'd double check if there were any issues or errors on your end before I wait another 12 hours for it to show as parsed and indexed.
>> Thank you!
>> -ben
>> 
>> http://bioportal.bioontology.org/ontologies/ECSO
>> 
>>> On Aug 18, 2016, at 8:42 AM, Ben Leinfelder <leinfelder at nceas.ucsb.edu> wrote:
>>> 
>>> That did the trick!
>>> 
>>>> On Aug 17, 2016, at 4:20 PM, John Graybeal <jgraybeal at stanford.edu> wrote:
>>>> 
>>>> Hi again Ben,
>>>> 
>>>> We have finished running the Annotations script, and annotations are now available for ECSO. Sorry for the trouble!  I'm not sure why this step was needed, but we'll keep that question for later.
>>>> 
>>>> Please give it a try.
>>>> 
>>>> John
>>>> 
>>>> 
>>>>> On Aug 17, 2016, at 3:37 PM, John Graybeal <jgraybeal at stanford.edu> wrote:
>>>>> 
>>>>> Thanks for the update Ben.
>>>>> 
>>>>> The Annotations may not have run successfully. We'll try re-running them, but I see these errors in the log:
>>>>> 
>>>>> 2016-08-15T10:21:36 [main] ERROR u.a.m.c.o.o.OWLOntologyManagerImpl - Illegal redeclarations of entities: reuse of entity http://www.w3.org/2004/02/skos/core#definition in punning not allowed [Declaration(AnnotationProperty(<http://www.w3.org/2004/02/skos/core#definition>)), Declaration(DataProperty(<http://www.w3.org/2004/02/skos/core#definition>))]
>>>>> 
>>>>> 2016-08-15T10:21:36 [main] ERROR u.a.m.c.o.o.OWLOntologyManagerImpl - Illegal redeclarations of entities: reuse of entity http://www.w3.org/2004/02/skos/core#altLabel in punning not allowed [Declaration(AnnotationProperty(<http://www.w3.org/2004/02/skos/core#altLabel>)), Declaration(DataProperty(<http://www.w3.org/2004/02/skos/core#altLabel>))]
>>>>> 
>>>>> This suggests that you may have used each of skos core#definition and core#altLabel properties in two different roles. I don't have time to confirm that, but if so I think Protege will detect the same issue. Good chance you'll need to fix that before the annotations work.
>>>>> 
>>>>> John
>>>>> 
>>>>>> On Aug 17, 2016, at 3:04 PM, Ben Leinfelder <leinfelder at nceas.ucsb.edu> wrote:
>>>>>> 
>>>>>> Hi John,
>>>>>> While the 'search' endpoint is working for me now, the 'annotator' endpoint is not returning any recommended concepts. 
>>>>>> For example:
>>>>>> https://data.bioontology.org/annotator?ontologies=ECSO&apikey=<KEY>&text=temperature
>>>>>> 
>>>>>> I've also tried the web UI - http://bioportal.bioontology.org/annotator - which also returned zero results.
>>>>>> 
>>>>>> Any ideas?
>>>>>> Thank you,
>>>>>> -ben
>>>>>> 
>>>>>>> On Aug 17, 2016, at 10:25 AM, Ben Leinfelder <leinfelder at nceas.ucsb.edu> wrote:
>>>>>>> 
>>>>>>> Hi John,
>>>>>>> Just wanted to let you know that I added another submission and the ontology parsed/indexed after ~day. Thanks for the tip.
>>>>>>> -ben
>>>>>>> 
>>>>>>>> On Aug 12, 2016, at 7:29 PM, John Graybeal <jgraybeal at stanford.edu> wrote:
>>>>>>>> 
>>>>>>>> Hi Ben,
>>>>>>>> 
>>>>>>>> You are correct there is something wrong with the current submission. As this took place close to the time we were conducting some maintenance, it is possible the maintenance interfered with the proper processing of the submissions. 
>>>>>>>> 
>>>>>>>> With the weekend upon us, I suggest starting with the simplest approach. Please try resubmitting your last submission to see if that succeeds this time.  If that doesn't work, please reply to the list, and we'll start looking under the hood.
>>>>>>>> 
>>>>>>>> john
>>>>>>>> 
>>>>>>>> 
>>>>>>>> 
>>>>>>>>> On Aug 12, 2016, at 1:57 PM, Ben Leinfelder <leinfelder at nceas.ucsb.edu> wrote:
>>>>>>>>> 
>>>>>>>>> Hello,
>>>>>>>>> I'm circling back to some UI development using the ECSO ontology - http://bioportal.bioontology.org/ontologies/ECSO - and I'm not getting results when I try to use the REST API. For example:
>>>>>>>>> https://data.bioontology.org/search?ontologies=ECSO&apikey=<KEY>&pagesize=1000&suggest=true&q=temperature
>>>>>>>>> 
>>>>>>>>> Could you take a look and see if something is awry? I see the ontology version for 8//03/2016 still has not been parsed or indexed, so perhaps that is a clue...
>>>>>>>>> 
>>>>>>>>> Thank you,
>>>>>>>>> Ben Leinfelder
>>>>>>>>> NCEAS informatics team
>>>>>>>>> _______________________________________________
>>>>>>>>> bioontology-support mailing list
>>>>>>>>> bioontology-support at lists.stanford.edu
>>>>>>>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>>>>>>> 
>>>> 
>>>> 
>>> 
>> 
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