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[bioontology-support] Old NCBO Annotators parameters ?

Ray Fergerson ray.fergerson at
Fri Dec 13 17:24:15 PST 2013



(Finally) responding to the pieces of this thread that others have not.


We have 400+ ontologies in BioPortal now and we don't think that running
an mgrep/ontology is really workable. Unfortunately, as you know, that
means that we cannot use the mgrep version of "longest only".  We would
have to duplicate this logic at the rest level. We have a bug open for


We removed scoring from the annotation process since it wasn't clear that
anyone was using this. We have a simpler scoring mechanism for ontology
recommendation but the value is not returned to the user. It is simply
used to help rank the top ontologies. Here it is not so much the score
that is important but simply the rough rank.




From: bioontology-support-bounces at
[mailto:bioontology-support-bounces at] On Behalf Of
Clement Jonquet
Sent: Monday, November 18, 2013 12:19 AM
To: support at
Subject: [bioontology-support] Old NCBO Annotators parameters ?


Hi all, 


Will the old NCBO Annotator parameters :






come back sometime in the new implementation of the Annotator ?


Also, what happen to the  Scored parameter, and more important, is there
any more scoring ?

This was quite important to distinguish annotations one another and to
aggregate them all.


Also, is the meaning of the new 'ontologies' parameter 

ontologiesToExpand or  ontologiesToKeepInResult ?

i.e., are you using all the ontologies to expand with mappings and then
keep only the results in the 'ontologies' parameter ? (remember the
"treatment" & "therapeutic procedure" example.







Dr. Clement JONQUET  -  PhD in Informatics  -  Assistant Professor

PI of the  <> SIFR project: Semantic Indexing of
French Biomedical Data Resources (ANR, UM2, CNRS)


 <mailto:jonquet at> jonquet at



                University of Montpellier                          Tel:
+33/4 67 14 97 43

Fax:                     +33/4 67  41 85 00           

                161 rue Ada
Skype:                 clementpro
                34095 Montpellier Cdx 5
Twitter:                <> @jonquet_lirmm

Google:                <mailto:jonquet.lirmm at>
jonquet.lirmm at






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