# OBO Training Materials Outline

digraph G {
  node[shape=none]
  "Ontology Term Use"
  "Diseases and Phenotypes" -> "Ontology Term Use"
  "Ontology Contribution" -> "Ontology Term Use"
  "RDF(S)" -> "Ontology Term Use"
  "OWL" -> "RDF(S)"
  "Linked Data Analysis" -> "OWL"
  "Application Ontology Development" -> "Ontology Contribution", "OWL"
  "Ontology Development Automation" -> "Automation", "Application Ontology Development"
  "Semantic Databases" -> "Application Ontology Development"
  "OBO Project Management" -> "Ontology Development Automation"
}

- Ontology Term Use
- context: using ontology terms in a document or spreadsheet
- skills
- know what ontologies are good for
- find good ontologies: ontology repositories, OBO
- find good terms: ontology browsers
- assess for use: license, quality
- map local terminology to ontology terms
- identify missing terms
- use IRIs, prefixes, CURIEs, labels
- use Protege?
- Ontology Contribution
- context: contribut terms to existing ontologies
- builds on: Ontology Term Use
- skills
- use GitHub: issues, Pull Requests
- understand basic Open Source etiquette
- reading READMEs
- understand basics of ontology development workflows
- understand ontology design patterns
- use templates: ROBOT, DOS-DP
- basics of OWL
- Ontology Theory
- context: learning more about SemWeb and OWL
- notes: maybe too big, split RDF and OWL?
- builds on: Ontology Term Use
- skills
- RDF
- RDFS
- OWL
- Reasoners
- basic SPARQL
- Turtle, JSON-LD
- Linked Data Analysis
- context: advanced queries with ontologies
- builds on: Ontology Theory
- skills
- advanced SPARQL
- term enrichment
- semantic similarity
- Named Entity Recognition
- more...
- Application Ontology Development
- context: combining ontology subsets for use in a project
- builds on: Ontology Theory, Ontology Contribution
- skills
- manage GitHub
- manage ontology imports
- use ROBOT extract: MIREOT, SLME
- use ROBOT report
- pruning trees
- Semantic Databases
- context: using ontology terms in a database
- builds on: Application Ontology Development
- skills
- advanced term mapping
- ontology terms in SQL
- terminology table JOINs, constraints
- convert tables to triples
- triplestores
- knowledge graphs
- Ontology Development Automation
- context: more technical side of ontology development
- builds on: Application Ontology Development
- skills
- Unix shell
- Make
- advanced git, GitHub
- ROBOT
- ODK
- OBO Reference Ontology Development
- context: leading a new or existing OBO project; maybe reference ontology develoment?
- builds on: Ontology Development Automation
- skills
- detailed knowledge of OBO principles and best practises
- use OBO Dashboard
- use OBO Registry
- use PURL system