1 of 29

OBO Academy:

Training materials for Bio-ontologists

Add name�Add location of talk

Date

2 of 29

What is the OBO Academy?

Design Philosophy

Available content

How to contribute to this effort

Overview

3 of 29

https://oboacademy.github.io/obook/

Introducing the

OBO Academy

Open, online, self-paced training materials
Repo is called OBOOK= Open Biological and Biomedical Ontologies (OBO) Organized Knowledge (OBOOK)
Aim to provide ongoing training for the ontology community that documents best practices in ontology development
Initially developed by our curation and semantic engineering team for the Critical Path Institute
This is a community resource, for the community, by the community

The OBO academy is an online resource that contains open, self-paced training materials that are intended to cover all aspects of ontology development and curation.
The content is available as a make docs website, and it is hosted in a github repository called OBOOK, which stands for Open Biological and Biomedical Ontologies (OBO) Organized Knowledge (OBOOK)
The goal of creating this resource is to provide document our workflows and best practices, and provide ongoing training for the ontology community
The project was initially developed by curators and semantic engineers from the OBO Fondry due to generous funding from the Critical Path Institute, a non-profit organization that uses semantic technolgies for drug development.
While these materials were initially created by our team, they are now intended to me a community resource - that are further developed and improved upon by the community.

4 of 29

A community of ontologists committed to a shared set of principles to build open biomedical ontologies

http://obofoundry.org/

5 of 29

Why did we create OBO Academy?

Needed to bridge this

Need well-documented and accessible training materials

Frequently asked questions

Image credit: https://vintageportland.wordpress.com/2010/08/06/st-johns-bridge-1930/

Siloed knowledge

Distributed expertise in our community

Technical
Curation
Domain

Knowledge is not always documented

Need to organize professional education in OBO

OBO resources
ICBO tutorials
Monarch tutorials
C-Path tutorial
…

Need to bridge this gap

So why did we create OBO Academy?
We initially developed a lot of the materials for a specific training course for employees at the critical path institute, but our funder generously allowed us to make all of the materials openly available to the community
We used this initial content to create the OBO Academy resource
This was a much needed resource because previously we had a lot of siioed knowledge amongst our community. Ontology development is a collaborative process and a lot of us had invidivudal knowledge in technical areas or curation expertise domain knowledge. However, all of our specialized knowledge was not always well documented, particularly in a centralized place
In our community, resources were available, for example, there are resources listed on the OBO Foundry website, there are tutorials offered every year at ICBO, the Monarch Initiative consortium has regular training sessions - but this is the first time that we’ve aggregated our collective knowledge into one place
Lastly, there are a lot of frequently asked questions that come up amongst the community, like how to set up Protege for ontology editing, how to use ODK, how to use ROBOT.
We needed to bridge this gap and create single source of knowledge that contains well-documented and accessible training materials

6 of 29

Database Curator

annotates datasets, experiments and publications with ontologies
requests new ontology terms
Suggests corrections to ontologies, such as wrong or missing synonyms, typos and definitions

Ontology Curator

develops and maintains ontologies
adds terms to ontologies
performs changes to ontologies, like adding or correcting synonyms
responsible for ontology releases

Ontology Engineer

Develops design patterns for ontologies that specify the logical structure of terms
responsible for ensuring the specification and consistent application of metadata in your ontologies
defines quality control checks

Ontology Pipeline Specialist

develops ontology pipelines with make and ROBOT
buildings release and QC architecture
builds infrastructure for application ontologies

Semantic Software engineer

uses ontologies to generate value to end-user applications
builds widgets that exploit the logical and graph structure of ontologies, e.g. phenotypic profile matching
builds ontology term browsers such as OLS

The different roles of OBO Semantic Engineering

The OBO Academy materials are meant to cater to a lot of different user groups. Some examples are shown here, but this is by no means exhaustive. For example, we have:

database curators, like the MOD curators, who annotate publications with ontology terms and make new term requests and report issues
ontology curators, who are involved in maintaining the content and iterative development of ontologies
ontology engineers who define QC checks and ensure consistency in the ontology
pipeline specialists who develop workflows and pipelines, such as using ROBOT templates and release workflows
and semantic software engineers who may be involved in using ontologies for software applications and user interfaces

this is not an exhaustive or exclusive list but merely some examples of users who may find these training materials useful

7 of 29

The OBO Academy content is intended to capture our collective knowledge and be a single resource where we can learn about ontology development

8 of 29

Design Philosophy

9 of 29

OBO Academy is a Community Effort

image credit: https://www.travelportland.com/events/waterfront-blues-festival/

There is not a set owner of these resource

Anyone is welcome to contribute

Create a community resource that is a single source of truth, to consolidate all our collective knowledge about ontology development best practices,workflows and background

GOALS

YOU are the editors

Continuously evolving resource

10 of 29

Key Features

Built in GitHub using Markdown
Website was created using Mkdocs
Purposely avoided using Powerpoint slides
Can easily search the documentations
Findable in google

https://oboacademy.github.io/obook/

11 of 29

Self paced learning materials

All training materials are intended to be self-contained to ensure that they can be studied without any further guidance by a teacher

Image credit: https://embracesomeplace.com/portland-oregon-best-parks/

12 of 29

https://diataxis.fr/

Content: Diátaxis framework

TUTORIALS

Learning-oriented material that contains exercises to help learners achieve basic competence in a specific area.

HOW TO GUIDES

Task-oriented guides that function as directions for specific tasks.

REFERENCE GUIDES

Information-oriented documentation that describes a single topic in a succinct, technical and orderly way.

EXPLANATIONS

Understanding-oriented documentation that clarifies, deepens and broadens the reader’s understanding of a subject.

13 of 29

Available content

14 of 29

Example content

https://drive.google.com/file/d/1CCQsOlUESw2KT5GL8CMSMLgxPPE9jaaH/view?usp=sharing

15 of 29

Example content:

Landing page

16 of 29

Example content:

Lesson

17 of 29

Example content:

Attribution for your contributions

18 of 29

Example content:

Lesson

19 of 29

Example content:

Exercises

20 of 29

Pathways

Ontology curator

Ontology curator GO-style
Ontology curator OBI-style

Ontology engineer/developer
Ontology contributor

Image credit: https://everout.com/portland/locations/forest-park-macleay-park-entrance/l30485/

21 of 29

Monarch Training

Biweekly training tutorials on zoom for members of the Monarch Initiative
Two approaches:

Flipped classroom approach where attendees review tutorials in advance
Trainers are available to answer questions

Demonstration/lecture on topics chosen by attendees
Discussion board to request topics and vote

22 of 29

How to contribute to OBO Academy

23 of 29

Content is available on GitHub
Community is needed to contribute

Update existing materials
Create new materials
Create issues on our tracker
Make requests for additional content
Community review of pull requests

New Lesson template is available

https://github.com/OBOAcademy/obook/

24 of 29

Unfamiliar with GitHub?

We have a ‘how to’ guide for that

https://oboacademy.github.io/obook/lesson/contributing-to-obo-ontologies/#use-github

Image credit: https://en.wikipedia.org/wiki/Laurelhurst_Park

25 of 29

Please edit!

Spot a typo? Please fix it.

26 of 29

Summary

Lack of documented ontology training materials

Consolidated knowledge that is for everyone

Open source materials for the community

We need YOU to contribute to the materials

Available content

Lessons, How to guides, Tutorials, Courses, Pathways….

Use our model

We encourage community members to use this model for documentation and training

Image credit: https://localadventurer.com/wp-content/uploads/2019/03/tom-mccall-waterfront-park-cherry-trees.jpg

27 of 29

Acknowledgements

Becky Jackson

Intelligent Medical Objects

Shawn Tan�European Bioinformatics Institute

Bradley Varner

European Bioinformatics Institute

James Overton

Knocean, Inc

Sabrina Toro

University of Colorado

David Osumi-Sutherland�European Bioinformatics Institute

Nico Matentzoglu

Semanticly

Nicole Vasilevsky

University of Colorado

28 of 29

Image credits

Cathedral Park/St John’s bridge (Slide 5): https://vintageportland.wordpress.com/2010/08/06/st-johns-bridge-1930/
Waterfront park (Slide 9): https://www.travelportland.com/events/waterfront-blues-festival/
Peninsula Park (Slide 11): https://embracesomeplace.com/portland-oregon-best-parks
Forest Park (Slide 16): https://everout.com/portland/locations/forest-park-macleay-park-entrance/l30485
Laurelhurst Park (Slide 20): https://en.wikipedia.org/wiki/Laurelhurst_Park
Cherry Blossoms/Waterfront Park: https://localadventurer.com/wp-content/uploads/2019/03/tom-mccall-waterfront-park-cherry-trees.jpg
Reed College Canyon (This slide): https://twitter.com/corsiaq/status/1277373837160542208

29 of 29

Thanks!

You can find me at:

[add email]

[add twitter handle]

https://oboacademy.github.io/obook/