# **Welcome** ### Introduction to Data Curation using Ontologies - FAIR Datasets and Community Collaboration The ways in which people encode meaning into text are complex. It is difficult to know for sure what one means without additional context. Semantic ambiguity can impede the sharing of knowledge and impact the comparability and interoperability of datasets. This course covers how we can use ontologies to improve the consistency and communication of ideas. Ontologies are data structures that are composed of controlled vocabularies, and the relations between them, that represent a piece of knowledge in a subject area. They are being used to support a variety of academic research, government, and commercial projects by providing findable, accessible, interoperable, and reusable (FAIR) data annotations that computers can reason over. This is a course not on how to develop an ontology, nor on the underlying data models, but rather on how a data curator can engage in ontology practices to support their FAIR data objectives. Over three sessions we will cover what ontologies are, how to access and explore ontologies, finding and evaluating appropriate ontology terms, annotating spreadsheet data, and how to make new term requests. We will introduce users to the Open Biological and Biomedical Ontologies (OBO) foundry community and their founding principles, as well as explore practical examples and applications using the Genomic Epidemiology Ontology (GenEpiO) and the Food Ontology (FoodOn). That being said, this course is not limited to individuals who work within genomic and epidemiological frameworks – our aim is to support users in solving practical data-quality problems using open access ontologies across disciplines. Several free and/or open-source tools will be introduced throughout the course, including but not limited to: Ontobee, EMBL-EBI Ontology Lookup Service, Protégé, and OntoMaton. --- **Audience:** Researchers, Data Curators **Original Course Dates:** July 26th-28th, 2022 **Total Length:** 3 hours (1 hr/session) + optional exercises --- **Level:** Beginner **Requirements:** This course is for beginners with no prior experience in ontologies, but basic computer skills are expected. Students will require a laptop with a functional keyboard and mouse. The computer does not require extensive processing power – any operating system will be fine, but it would be best if they had a mainstream browser (e.g. Chrome, Edge, Safari). We will be using free tools and google sheets for our activities. Offline tool downloads will not be required to participate and complete the course. **Course Learning Objectives** At the end of the course, participants will be able to: What is Fair What ontologies are and how they support FAIR objectives How to access and explore ontologies Finding and evaluating appropriate ontology terms during data curation How to make requests for new terms and term changes Practical automation for annotating spreadsheet data **Course Topics** This course will be presented over three days for 1 hour each day and will cover these topics: - Data curation - Ontology - FAIR - Reproducibility - Interoperability This course focuses on health sciences, genomics, and epidemiology in a public health framework, but our aim is to support users across disciplines. --- ![enter image description here][1] This course was made by the [Centre for Infectious Disease Genomics and One Health][2] (CIDGOH), affiliated with the [Faculty of Health Sciences][3] at [Simon Fraser University][4] (SFU), Burnaby, BC, Canada. The authors respectfully acknowledges the unceded traditional territories of the Coast Salish peoples, including the səl̓ilw̓ətaʔɬ [(Tsleil-Wautu][5]), kʷikʷəƛ̓əm ([Kwikwetlem][6]), Sḵwx̱wú7mesh Úxwumixw [(Squamish][7]) and xʷməθkʷəy̓əm [(Musqueam][8]) Nations, on which SFU and the CIDGOH laboratory is located. [1]: https://www.sfu.ca/content/sfu/communicators-toolkit/guides/brand-guide/on-brand-templates/email-signature/jcr:content/main_content/image_1603663121.img.2000.high.png/1602084740581.png [2]: http://www.cidgoh.ca [3]: https://www.sfu.ca/fhs.html [4]: https://www.sfu.ca/ [5]: https://twnation.ca/ [6]: https://www.kwikwetlem.com/ [7]: https://www.squamish.net/ [8]: https://www.musqueam.bc.ca/