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[bioontology-support] OBA and recommender in VA do not work properly

Michael Dorf mdorf at
Tue Feb 16 14:50:21 PST 2016

Hi Vincent,

It sounds like either your mgrep dictionary file or the annotator database did not get created successfully. You can re-run this process by executing the following command (substitute "GO,STY,NCIT" with your own comma-separated list of ontology achronyms:

 ~/dev/ncbo/ncbo_cron> ./bin/ncbo_ontology_annotate_generate_cache -o GO,STY,NCIT -r -d -l logs/annotator_cache.log

-r - delete the old annotator database
-d - re-generate mgrep dictionary file

Hope this helps!



> On Feb 13, 2016, at 07:00, vincentguo <gjw_0418 at> wrote:
> Hi NCBO BioPortal Team,
>  Recently I ran the VA with VMware Workstation and everthing went on well
> except that the OBA and recommender cannot work as expected. I chose several
> parsed ontologies, including the STY ontology, in OBA and recommender, and
> input a paragraph that contains terminologies coming from the chosen
> ontologies. As a result, only terminologies in STY Ontology were annotated
> and STY Ontology was recommended whereas others can't be identified. I
> worked a long time and couldn't find the reason. Could you please give me
> some advide on how to figure it out? 
> Looking forward to hearing from you.
> Kind regards,
> Vincent
> --
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