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[bioontology-support] [bioontology-curator] Question Regarding BioPortal Annotation Service

Ray Fergerson ray.fergerson at stanford.edu
Tue Jun 18 15:45:16 PDT 2013


Zach,

 

Sorry for the delay in responding. Your email got swept into the
"curators" list.

 

When I search for "New York" with the Gazetteer Ontology, I do not get a
concept that returns the "State of New York", which would be the correct
concept that I am looking for. The annotator service only returns concepts
that have a preferred label of "York"

 

This is correct. The annotator matches the entire label for a term to the
text passed in. Only exact matches are present. Thus the label  "State of
New York" will not match the text "New York" because the entire text of
the term label in not present in the text.

 

Similarly, when I search for the concept "Northern Highlands Lake
District" I do not get the correct concept "Northern Highland" but instead
get concepts  "Highlands" and "Lake District". 

 

The annotator does not do stemming. It does a simple string comparison.
Thus "Highlands" will not match "Highland".

 

Is this an error from the Annotator Service, or is this because how the
lexical matching of a keyword to a candidate concept is performed? Would
there be a way to improve the matching to include this concept, or a
parameter that I could set that would return ALL possible substring
matches? 

 

We don't have any such parameters. The goal of this particular annotator
is to be very fast and it uses a very simple "concept recognizer".

 

Ray

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