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[bioontology-support] Few VA related questions

Clement Jonquet jonquet at
Thu Mar 20 08:55:25 PDT 2014

Hi all, 


We have been starting to use our local VA and getting ready to change the
Annotator code inside.

We have a few questions for which answers ca save us long time ;) :


1.       Where do you suggest to check out the code from at the beginning ?
>From the NCBO GitHub or directly from the VA files? For instance, if we want
to change the \bioportal_web_ui project to update the UI of our local BP.
Should we get:  or 

/srv/rails/BioPortal/releases/bioportal_web_ui on the VA  or

somewhere else ?

The idea is to avoid any conflict if the code on GitHub is more recent than
the one executed on the VA.


2.       What do you guys use for automatic deployment from GitHub to stage
or production BP ? Maeven, or alike. any place we should look into on the


3.       Where are we defining groups and categories for our ontologies ?


4.       Is there an admin interface (more advanced that the admin login)
that enable to see what's going on with the parsing of ontologies.. i.e.,
where to look if the parsing of an ontology fails to clean up or debug.
Maybe also define groups, etc.


5.       Where should we look if we want to change what's happening
automatically when an ontology is added to BP via the UI. We specifically
are interested in the MGREP dictionary creation step that we want to
separate by "group". in order to create/update a group specific dictionary
file (in order for us to have 2 annotator on the same VA) ? 


Thank you by advance :)

Clement, Emmanuel and Soumia




Dr. Clement JONQUET  -  PhD in Informatics  -  Assistant Professor

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

Organizer of  <> Web Science
Montpellier Meetup


 <mailto:jonquet at> jonquet at



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