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[bioontology-support] Questions about NCBO status and BioPortal

Jeff Lerman jeff.lerman at invitae.com
Wed Aug 7 10:46:44 PDT 2019


Hello Jennifer,

Thanks very much for your detailed reply!  Much appreciated.  After our
developers have had a chance to review, we may be in touch with more
questions - but it’s great to have the overview & information you laid out.

Best,
—Jeff Lerman




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Jeff Lerman

AI Scientist

Mobile: 510-495-4621

www.invitae.com

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On Tue, Aug 6, 2019 at 3:20 PM Jennifer Leigh Vendetti <
vendetti at stanford.edu> wrote:

> Hello Jeff,
>
> Apologies for the late reply.
>
> This is a partial response to some of your questions. Will post another
> message to address the rest of your questions - hopefully by later today or
> tomorrow morning.
>
>
> On Aug 2, 2019, at 3:47 PM, Jeff Lerman <jeff.lerman at invitae.com> wrote:
>
> … I’m curious about the state of development of NCBO’s Annotator.  When
> was AnnotatorPlus Beta made available?
>
>
>
> AnnotatorPlus was developed externally to Stanford, mostly by Andon
> Tchechmedjiev, and other collaborators from LIRMM: http://www.lirmm.fr/.
> They contributed the work back to us, and we made it available in
> production BioPortal on May 29th of this year:
> https://github.com/ncbo/bioportal_web_ui/releases/tag/v5.7.1. However,
> it’s worth noting that our collaborators tested and were using this
> functionality in their own installation of BioPortal prior to May.
>
>
> Do you consider it to be stable, and is it undergoing active development?
>
>
>
> Yes, we consider it stable as it builds on Annotator functionality that
> has been around for a long time. We’ve had no bug reports from the user
> community since the May release.
>
> We’re working on other higher priority things at the moment, but
> AnnotatorPlus is on our radar as something we’d like to move from beta to
> official production.
>
>
> Does the code posted at GitHub <https://github.com/ncbo/ncbo_annotator> correspond
> to Annotator or AnnotatorPlus (or neither)?
>
>
>
> The front-end code for the page you see in the BioPortal application (
> https://bioportal.bioontology.org/annotatorplus) is publicly available in
> the bioportal_web_ui repository (https://github.com/ncbo/bioportal_web_ui).
> It’s a Rails application, so the code is located in the various standard
> Rails directories, i.e.:
>
>
> https://github.com/ncbo/bioportal_web_ui/blob/master/app/assets/javascripts/bp_annotatorplus.js
>
> https://github.com/ncbo/bioportal_web_ui/blob/master/app/controllers/annotatorplus_controller.rb
>
> https://github.com/ncbo/bioportal_web_ui/blob/master/app/views/annotatorplus/index.html.haml
>
> The Annotator code is available in the ncbo_annotator repository:
> https://github.com/ncbo/ncbo_annotator.
>
> The AnnotatorPlus code is available in a repository external to the NCBO
> GitHub organization: https://github.com/sifrproject/annotators.
>
> Our instance of AnnotatorPlus is currently running as a Java Servlet,
> calling the BioPortal REST API behind the scenes. As time allows, our plan
> is to move away from this model and integrate the AnnotatorPlus
> functionality into the same codebase we use for the BioPortal REST API. Our
> REST API is developed in Ruby - all of the code is open source and is
> encapsulated by several repositories in the NCBO GitHub organization, e.g.,
> ontologies_api, ontologies_linked_data, etc.
>
> Hope that information helps.
>
> Kind regards,
> Jennifer
>
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