Search Mailing List Archives

Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] Annotator query

Clement Jonquet jonquet at
Fri Dec 14 06:51:05 PST 2012

Hi Eamonn, 


To my knowledge, this is normal (maybe not expected) behavior.

The Annotator will get matches that are “smaller” or “exactly” equal (only exactly if using longestOnly=true) but not matches that are longer.


Otherwise a piece of text containing “melanoma” will be annotated with any kind of melanoma (e.g., skin melanoma, eye melanoma, etc..) which will be bad. In your case, what you want to use is the BioPortal search service ( that will get you the match “compound treatment design” in OBI for instance.


I know this might seems weird, but this is intrinsically what make the differences between “search” and “annotate” ;)


Hope it helps




Dr. Clement JONQUET  -  PhD in Informatics  -  Assistant Professor

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


jonquet at 


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

                LIRMM                                                                Fax:                        +33/4 67  41 85 00           

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

                France                                                                 Google:               jonquet.lirmm at





De : bioontology-support-bounces at [mailto:bioontology-support-bounces at] De la part de Eamonn Maguire
Envoyé : mercredi 12 décembre 2012 13:18
À : support at Support
Cc : isatools at
Objet : [bioontology-support] Annotator query


Hi all, 


I have a query about the annotator. 


It appears that if we search on something like "compound treatment", we don't get a hit for "compound treatment design" for instance from OBI/EFO. Do you have any idea about how we can get the search results to return a better match? Or if it's possible?


Many thanks,





Eamonn Maguire
Oxford e-Research Centre & Computer Science Department

University of Oxford


7 Keble Road, Oxford, OX1 3QG

T: 01865 (2) 610788 M: 07526 924483


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <>

More information about the bioontology-support mailing list