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ncbo / ncbo_annotator

To automatically process a piece of data text to annotate it with relevant ontology concepts and return the annotations.
http://bioportal.bioontology.org/annotator
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Result sets include classes that no longer exist in latest submission #7

Open jvendetti opened 5 years ago

jvendetti commented 5 years ago

To reproduce, execute the following REST call that includes ancestors specified to 3 levels deep:

http://data.bioontology.org/annotator?text=Melanoma%20is%20a%20malignant%20tumor%20of%20melanocytes%20which%20are%20found%20predominantly%20in%20skin%20but%20also%20in%20the%20bowel%20and%20the%20eye.&ontologies=MEDLINEPLUS&expand_class_hierarchy=true&class_hierarchy_max_level=3

In the resulting JSON, there's one ancestral annotatedClass object with distance of 2 that no longer exists in the latest submission of the MEDLINEPLUS ontology. Screenshot of particular result:

Screenshot 2019-10-03 14 40 03

Clicking on the "self" link results in a 404 error:

"Resource 'http://purl.bioontology.org/ontology/MEDLINEPLUS/C1456590' not found in ontology MEDLINEPLUS submission 13"

@alexskr performed a full regeneration of the Annotator cache for all ontologies on Oct. 2nd. I checked the log file on the production parsing box (/srv/ncbo/ncbo_cron/logs/cache.log) and see no errors for the MEDLINEPLUS ontology:

I, [2019-10-02T22:08:06.271420 #22045]  INFO -- : Creating Annotator cache for http://data.bioontology.org/ontologies/MEDLINEPLUS (http://data.bioontology.org/ontologies/MEDLINEPLUS/submissions/13) - 1142/1238 ontologies
I, [2019-10-02T22:08:06.333339 #22045]  INFO -- : ["Caching classes of MEDLINEPLUS"]
I, [2019-10-02T22:08:07.448444 #22045]  INFO -- : ["Page 1 of 1 - 2258 classes retrieved in 1.110196227 sec."]
I, [2019-10-02T22:08:20.611879 #22045]  INFO -- : ["Page 1 of 1 cached in Annotator in 13.163305221 sec."]
I, [2019-10-02T22:08:20.703788 #22045]  INFO -- : ["Completed caching ontology: MEDLINEPLUS (http://data.bioontology.org/ontologies/MEDLINEPLUS/submissions/13) in 14.278680390212685 sec. 2258 classes."]

A side effect of this issue is that our example code for working with the Annotator throws exceptions - so far noticed by at least one end user (see: https://github.com/ncbo/ncbo_rest_sample_code/issues/5)