Skip to content

Overview

Lessons

Using Ontologies and Ontology Terms

  • Target roles: Database Curators
  • 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 terms to ontology terms
    • identify missing terms
    • use IRIs, prefixes, CURIEs, labels
    • use Protege?

Contributing to OBO ontologies 1: Protege and Github

  • Target roles: Database Curators, Ontology Curator, Ontology Engineer/Developer
  • Builds on:
  • 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 Fundamentals

  • Target roles: Ontology Curators, Ontology Engineer/Developer
  • Builds on:
  • Skills:
    • RDF
    • RDFS
    • OWL
    • Reasoners
    • basic SPARQL
    • Turtle, JSON-LD

Linked Data Analysis

  • Target roles: Ontology Curators, (Semantic) Software Engineer
  • Builds on:
  • Skills:
    • Advanced SPARQL
    • Term enrichment
    • Semantic similarity
    • Named Entity Recognition
    • more...

Ontology Development

Semantic Databases

  • Builds on:
    • Ontology Development
  • skills
    • advanced term mapping
    • ontology terms in SQL
    • terminology table JOINs, constraints
    • convert tables to triples
    • triplestores
    • knowledge graphs

Automating Ontology Development Workflows

  • Builds on:
    • Ontology Development
    • Ontology Pipelines
  • Skills:
    • Unix shell
    • make
    • Advanced git, GitHub
    • ROBOT
    • ODK

Developing an OBO Reference Ontology

  • Builds on:
    • Ontology Development Automation
  • Skills:
    • Detailed knowledge of OBO principles and best practises
    • Use OBO Dashboard
    • Use OBO Registry
    • Use PURL system

Tutorials

How-to guides