Web service to add functionalities to the http://bioportal.bioontology.org and similar ontology annotators
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sifr-bioportal-annotation-model
sifr-bioportal-annotation-postannotations
sifr-bioportal-annotator-client
sifr-bioportal-annotator-proxy
sifr-bioportal-annotator-scoring
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README.md
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sifr-bioportal-annotator-submodule-template.zip

README.md

AnnotatorPlus and LIRMM Annotation Proxy

Initial Author: Julien Diener

Project heads: Clement Jonquet and Pierre Larmande

CValue Scoring Vincent Emonet, COnTeXT integration Amine Abdaoui

Architectural refactoring: Andon Tchechmedjiev

Includes work from: Soumia Melzi and Emmanuel Castanier

Deployment

  • branch master to deploy to /annotator, for the LIRMM Bioportal Annotator Proxy with Bioportal running on the same server
  • branch ncbo_annotator to deploy to /ncbo_annotatorplus to add post-annotation capabilities to the NCBO BioPortal Annotator

Development

This project is structured as a multimodule maven project and requires maven for development. It is recommended to use and IDE that includes built-in maven support. As of 2016, NetBeans can have some issues with complex maven projects, it is therefore advisable to use Eclipse or IntelliJ.

Project structure

The modules of the project are the following:

  • sifrbioportal-bioportal-annotation-model: This is the core module of the project. It implements a custom (non-standard) JSON-LD datamodel matching that of NCBO bioportal and adds additional annotation capabilities matching additional post-processing annotations implemented in the proxy, as well as input/output capabilities from and to various formats.

Local dependencies

Some localdev dependencies are required and can be found in the localdev-dep folder. The dependencies will be installed automatically upon performing mvn clean install for the first time.

Note that eclipse does not automatically update the eclipse project upon changes in the pom.xml files, you may need to update the project manually:

  • in the command line, execute mvn eclipse:eclipse
  • close and reopen your project

Testing deployment