Editor tools guide

This page describes some of the tools used to edit generate parts of the ontology and keep them in sync with external resources.

Ontology Editing

For editing we use a mixture of emacs (for editing the core module) and Protege (for editing the phenoscape-ext.owl extension, and for exploring and debugging).

The original version of Uberon was developed using OBO-Edit, but we no longer use this for editing.

• Protege 4
  • OBO Plugins
  • ELK plugin
• Emacs
  • obo-mode.el
  • macros
• OBO-Edit

Ontology Build Pipeline

For the production build pipeline we use owltools and a Jenkins Continuous Integration (CI) environment. OWLTools comes bundled with the magnificent Elk.

• owltools
• ELK plugin

Ontology Alignment and Text Processing

Historically we have used blipkit prolog framework for text processing

• blipkit
  • Obol
  • metadata_nlp

These are all controlled by the Makefile in the Uberon directory

• Makefile

Many of these tools are highly adapted to the task at hand, and may not translate well to other ontology alignment tasks. Others are welcome to use these, but caveat emptor.

We are moving away from this framework to use owljs, and in particular the owljs implementation of Obol

• https://github.com/cmungall/owljs
  • Obol.js