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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:
  • 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 Fundamentals

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

Linked Data Analysis

  • Target roles: Ontology Curators, (Semantic) Software Engineer
  • Builds on:
  • Ontology Fundamentals
  • 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