Planteome Protege/OWL Course, Corvalis, November 2015

The main goal of the tutorial is have participants understand the principles of developing OWL ontologies, how classes can be combined together, how a reasoner can be used for auto-classification and error-checking.

Intro

• presentations/Protege-OWL-Intro.pptx

Tutorial

The tutorial text is here

• presentations/protege_planteome_tutorial.doc

We will work through the following examples. Each section introduces new constructs and/or concepts.

For each section, the instructor will first demonstrate some examples. The students will then follow the instructions in the README.txt file for the section. After completion, the students can exchange OWL files and review one another's work.

Basics

• basic-subclass

  Task: build a basic hierarchy Constructs: SubClass, annotations Uses reasoner: None Ontology: cell component (subset)

• basic-restriction

  Task: add part_of restrictions to ontology Constructs: SubClass, ObjectProperty, "some" (existential restriction) Uses reasoner: None Ontology: cell component (subset)

• basic-dl-query

  Task: perform queries using class expressions Constructs: and, some Uses reasoner: Hermit Ontology: cell component (subset)

• basic-classification

  Task: use reasoner to build hierarchy Constructs: SubClass, "some", Equivalence, "and" (intersection) Uses reasoner: Hermit Ontology: cell component (subset)

Optional

• disjoint-expressions

  Note: the instructor may use this one as an example Task: create spatial disjointness axioms without the use of helper "X part" classes Constructs: General Axioms Uses Reasoner: Hermit

• basic-disjoint

  Task: find problems in ontology Constructs: DisjointWith Uses reasoner: Hermit Ontology: cell component (subset)

• taxon-union

  Task: create taxonomic grouping classes Constructs: or, not Uses reasoner: Hermit Ontology: NCBITaxon (subset)

• occurs-in

  Note: the instructor may use this one as an example Task: examine how to compose relations to get desired inferences Constructs: property chains Uses Reasoner: Hermit Ontology: BP and CC (subset)

• regulation-classification

  Task: examine how to compose relations to get desired inferences Constructs: property chains Uses Reasoner: Hermit Ontology: BP (subset)

• response-to-stimulus

  Task: use an external ontology for classification Constructs: owl:imports Uses Reasoner: Hermit Ontology: BP (Subset) and import of Stimulus ontology

• advanced-metabolism

  Note: We may skip this one until day 2 Task: use an external ontology for classification, together with helper axioms Constructs: owl:imports, property chains Uses Reasoner: Hermit or Elk Ontology: BP (Subset) and import of Chebi plus extras

• obo-owl-classification

  Task: edit an ontology in OE and classify in Elk Uses Reasoner: Hermit Requires: OE 2.1.1beta4 or higher