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Learning Ontologies

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Krishna Udaiwal edited this page Nov 9, 2021 · 1 revision

[DRAFT]

There are 2 paths towards likely teaching Ontologies as a subject to incoming students. Its divided into working with the data or the tools, where the former refers to being the curator, and the latter being the engineer. These roles and a great tutorial, by one of the leading organizations in Ontologies, can be found here: https://oboacademy.github.io/obook/getting_started/.

Now, in order to focus on the data aspect, there are further 2 distinct paths, that of the curator and a user. The curator edits and modifies a specific Ontology while a user reads and analyzes the information for use in various capacities. The workflow documentation for the curator can be found partially in the tutorial above and in the specific Ontology repo pages, incl,

  1. https://github.com/KrishnaTO/agro/blob/master/CONTRIBUTING.md
  2. https://github.com/AgriculturalSemantics/agro/blob/master/src/ontology/README-editors.md

In regards to a user's workflow, there are limited resources within our sphere, but generally can be categorized into working manually with Protege (primary application for Ontologies) or Programming Languages (R/Py) libraries (bioconductor::rols, others to be located). The methods to use the former are the subject of most webinars and other tutorials on youtube, while the latter require more effort. The special tools and browsers are also a part of all divisions' arsenal, which include term browsers (OLS, OntoBee, BioOntology, etc) and searching tools (BioOntology's Annotator, OLS's ZOOMA, etc).

For the role of the engineer, there are a plethora of different tools that are preferred, with more advanced tools being developed encompassing the bases. For a great list, there are 2 pages:

  1. http://obofoundry.org/resources
  2. https://oboacademy.github.io/obook/reference/semantic_engineering_toolbox/
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