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[bioontology-support] Questions about NCBO status and BioPortal

Jennifer Leigh Vendetti vendetti at stanford.edu
Tue Aug 6 15:19:54 PDT 2019


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<mailto: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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