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[bioontology-support] OBA restrictions

Samson Tu swt at
Fri Apr 27 18:15:34 PDT 2012

> On Apr 25, 2012, at 3:44 AM, Clement Jonquet wrote:
>> Concerning the views, as far as I know the ontology views are not 
>> grabbed in the backend DB.
>> In order to avoid having to many annotations generated by the 
>> Annotator workflow (also used for the NCBO Resource Index) we have 
>> decided in the past to make available only the latest version of 
>> ontologies and not views, although it is technically possible. Trish 
>> and Ray will confirm if this stamen is still true today.

Also, I can understand the policy of not using views when the task is to 
create the Resource Index. However, my task is to annotate a particular 
document using a particular ontology. It seems that it would make sense 
to allow the user to choose either the ontology or one of its views.

I don't understand the following restriction:
Attention, if the Annotator finds an annotation with the complete phrase 
in an ontology composing the dictionary, partial annotations with other 
ontologies will not be generated. For example, because/breast 
cancer/exists in Human Disease and the NCI Thesaurus, 
if/longestOnly=true/, annotations generated with those terms will block 
annotations with the terms/breast/in the Vaccine Ontology or/cancer/in 
BIRNLex. For this reason, we discourage the uses of 
the*longestOnly*parameter when the Annotator is used with one or a small 
number of ontologies.

Why is the "longestOnly" parameter disallowed when the annotator is used 
with one ontology? The explanation doesn't make sense when only one 
ontology is involved. Suppose NCI Thesaurus is the ontology we want to 
use and it matches "breast cancer", we don't care whether the Vaccine 
ontology,  BIRNLex, or any other ontology match "breast" or "cancer." We 
only care about NCI Thesaurus matches.


Samson Tu                                   email: swt at
Senior Research Scientist                   web:
Center for Biomedical Informatics Research  phone: 1-650-725-3391
Stanford University                         fax: 1-650-725-7944

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