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How do I browse an ontology?

Browsing an ontology can be tricky for newcomers. There are lots of files, scripts, directories, strange terms, and technological corridors to walk down. This guide will help you find the main ontology file and browse for terms.

Browsing ELMO with Protégé

The gold standard for searching and editing ontologies is the free software package called Protégé.

New software can be a bit daunting, but is worth the effort. It's free, lightweight and easy to install. You can also use the web version - WebProtégé, but it handles ontologies a bit differently and imports may not work properly. That means some terms may be reduced to their CURIE, which may make it difficult to browse.

Here is a very quick and easy document on how to start and work with Protégé: Protégé Documentation: Getting started

One key step is knowing how to locate the proper file to open. The GitHub repository contains lots of files that are different "translations" of the ontology into varied data formats. You don't need to worry about any of these. The only file you want is elmo.owl. It can be downloaded at this link (right click and select "save as").

Browsing ELMO in HTML

There are two HTML versions of ELMO that you can look at. The basic version can always be found at the permanent URL for ELMO: https://w3id.org/elmo

That version contains only terms that originate in ELMO. There will be no imported terms.

For much more information, you can see another page auto-generated by PyLODE here: https://timalamenciak.github.io/elmo/lode.html

Browsing ELMO on BioPortal

We will upload a version of ELMO to BioPortal once a full release is finished.

How to browse other ontologies

Most domain ontologies (and every OBO Foundry ontology) can be found on an ontology indexing site. These sites gather and index ontologies. They often provide the best searching and viewing experience next to installing Protégé. In addition, they allow you to quickly click between ontologies and may reveal connections and terms relevant to your work.

Here is an incomplete list of these indexing sites:

You can also check out the Awesome Ontology list for more tools.