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[bioontology-support] Old NCBO Annotators parameters ?

Clement Jonquet jonquet at
Tue Nov 26 04:54:46 PST 2013

Hi Manuel, 

Thanks for your responses.

See some remarks in green. 




De : manuelso [mailto:manuelso at] 
Envoyé : jeudi 21 novembre 2013 18:22
À : Clement Jonquet
Cc : support at Support
Objet : Re: [bioontology-support] Old NCBO Annotators parameters ?


Hi Clement,


I think some of your points here come from incomplete documentation that we
need to fix. Thanks for pointing these out.


There are a couple of questions that need investigation, the ones with
tickets created. I will respond to them once we learn what the solution is.


Find answers inlined below.





On Nov 18, 2013, at 12:18 AM, Clement Jonquet <jonquet at
<mailto:jonquet at> > wrote:

Hi all,


Will the old NCBO Annotator parameters :



This parameter was removed due to inability to perform longestOnly on a set
of ontologies. mgrep does longest work across the entire dictionary.

==> Can you take the occasion of the new release to have “one mgrep per
ontology” as it was discussed a few years ago ? Mgrep is intentionally
designed to be run with several daemons in parallel (see doc).

This feature is quite missing for anyone who want to reduce the number of
annotation returned by a picece of text.

(We have e.g., someone at LIRMM (Sandra) who is interested in matching the
longest term only).



We do not have this flag at the moment and I am not sure of what the
expected behavior is here. I have created a ticket to investigate this.


==> Not documented at :




became exclude_numbers


==> Not documented at :




became minimum_match_length


==> Yep, sorry I forgot to remove this one when wrote the email ;)




By default include synonyms but I believe we do not have a flag to disable
this at the moment. I have created a ticket to address this issue.


==> Ok, thanks Could be useful maybe. 


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 ?


The scoring was removed. I all ask Ray to comment on this.

==> Ok. If you can provide more information about this then I am interested.
By the way, I a am working with Juan a student of mine using an NLP measure
that I am thinking about using to enhance scoring (based on the term
embedded in longer terms and frequency). I can discuss this off list you you


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 ?


The ontologies param aligns with the old ontologiesToKeepInResult. To expand
one needs to use the class endpoints.


I don’t understand the second part of the response, could you elaborate a
bit more ? 

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)


jonquet at <mailto:jonquet at>


                University of Montpellier                          Tel:
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