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Navigating ENVO

Kai Blumberg edited this page Nov 29, 2020 · 42 revisions

Large ontologies such as ENVO can be difficult to understand or navigate upon first glance. As such we have created this guide about how to navigate envo, as well as what types of classes exists within the ontology.

Table of contents

View ENVO on the web

View ENVO in protégé


Viewing ENVO

View ENVO on the web

The simplest way to browse ENVO is through the Ontology Lookup Service (OLS) envo browser. In the OLS web browser you can search for terms by their labels (or identifiers). For example, typing in rock, one would see the following:

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Next you can navigate to a term such as rock:

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You can use OLS to further explore a terms subclasses in the Tree view tab by expanding it by clicking on the image sign next to a term. From there you can continue to explore the hierarchy by expanding and collapsing sub-hierarchies.

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View ENVO in protégé

A more advanced way to browse ENVO, which enables users to view and drill down on the entire file at once is to download protégé. Once installed click File, then Open from URL....

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Then in the URI box paste in http://purl.obolibrary.org/obo/envo.owl, and click OK.

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Next click on the Entities tab.

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You can click on the small triangles image next to terms in order to expand them and see what's below.

The top level classes can be a little confusing to follow so see the ENVO Hierarchies section about where to navigate to in order to get started. At any time in protégé you can search for classes by name or ID, by typing control and f on windows or command and f on a mac. This will bring up a search box in which you can type into.

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ENVO Hierarchies

At the very top of the ENVO hierarchy you'll find the terms continuant and occurrent.

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These terms are from the Basic Formal Ontology (BFO), which is the upper level ontology that ENVO uses. There are quite a few details about how BFO represents and divides up various concepts. The very top most level classes are explained as follows: Continuants are classes that don't change over time, e.g., a wine glass. Occurrents are classes which unfold overtime, e.g., a glass blowing process.

In order to keep things simple rather than explain more about BFO, the following sections highlight the important hierarchies within ENVO. These are the places to start when searching for ENVO terms.

Material entity

Environmental material

Astronomical body part

biome

environmental system process

Quality

Site