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[bioontology-support] OBA restrictions
swt at stanford.edu
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 stanford.edu
Senior Research Scientist web: www.stanford.edu/~swt/
Center for Biomedical Informatics Research phone: 1-650-725-3391
Stanford University fax: 1-650-725-7944
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