On becoming an OBO Semantic Engineer¶
Welcome to the OBOOK and our OBO Semantic Engineering Training!
Introduction to the OBOOK (Open Biological and Biomedical Ontologies Organized Knowledge)¶
Documentation in the OBOOK is organised into 4 distinct sections based on the Diátaxis framework of documentation:
- Tutorials: Learning-oriented documentation that contains exercises to help a beginner achieve basic competence in a specific area.
- How-to Guides: Task-oriented documentation that functions as directions to guide the reader through the steps to achieve a specific end.
- 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.
To accommodate for the various training use cases we support, we added the following categories:
- Courses: A convenience content type that assembles materials from OBOOK for a specific, taught unit, such as the yearly ICBO tutorials.
- Pathways: A kind of course pertaining to a specific role in the OBO-sphere, such as curator or software developer.
- Lessons: A collection of materials (tutorials, explanations and how-to guides) that together aim to teach a well defined concept.
Note: We are in the process of transforming the documentation accordingly, so please be patient if some of the documentation is not yet in the correct place. Feel free to create an issue if you find something that you suspect isn't in place.
- James Overton, Knocean Inc. James has been a developer of software to support ontology development in and around the OBO sphere for more than a decade and delivers services to the OBO community through his company, Knocean Inc.
- Becky Jackson, Bend Informatics. Becky has been a Semantic Software developer and Ontology Pipeline specialist since 2016, now working as an independent consultant.
- Nicole Vasilevsky, Critical Path Institute. Nicole is the Associate Director of Data Science and an Ontology Curator for the Mondo Disease Ontology, and contributes to several other ontologies including the Human Phenotype Ontology, Uberon Anatomy Ontology, and Cell Ontology.
- Nicolas Matentzoglu, Semanticly, Athens, Greece. Nico is an Ontology Engineer and Ontology Pipeline Specialist, being the Principal Ontology Pipeline Developer for the Monarch Initiative.
- Shawn Tan, EMBL-EBI. Shawn is an Ontology Curator for The Brain Data Standards project.
- Bradley Varner, EMBL-EBI. Bradley is an Ontology Curator for the Cell Annotation Platform.
If you would like to contribute to this training, please find out more here.
- Getting started (read this first)
- Course overview and lessons
- How to contribute
- Getting started for OBOOK documentation writers
Critical Path Institute¶
Critical Path Institute (CPI) is an independent, nonprofit organisation dedicated to bringing together experts from regulatory agencies, industry and academia to collaborate and improve the medical product development process.
In April 2021, the CPI has commissioned the first version of this OBO course, contributing not only funding for the preparation and delivery of the materials, but also valuable feedback about the course contents and data for the practical exercises. We thank the CPI for contributing significantly to the OBO community and open science!