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[bioontology-support] Old NCBO Annotators parameters ?

manuelso manuelso at
Thu Nov 21 09:21:52 PST 2013

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> wrote:

> Hi all,
> Will the old NCBO Annotator parameters :
> longestOnly

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

> wholeWordOnly

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.

> filterNumber

became exclude_numbers

> minTermSize

became minimum_match_length

> withSynonyms

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.

> 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.

> 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.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.
> Bye
> Clement
> ----------------------------------------------------------------------------------------------------------------------
> 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          
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