Description
Table of ContentsChapter 1: Introduction1. Who is this book for?2. Why ontologies?3. Why Python?4. Why Owlready?5. Book outline6. Acknowledgements
Chapter 2: Python Language: Adopt a Snake! 1. Installing Python2. Starting Python3. Syntax 4. Main datatypes5. Conditions (if)6. Loops (for) 7. Generators8. Functions (def) 9. Classes (class) 10. Python modules11. Installing Owlready212. Summary
Chapter 3: OWL Ontologies 1. An ontology... what does it look like?2. Creating ontologies manually with the Protégé editor3. Example: An ontology of bacteria4. Creating a new ontology• Classes• Disjoints• Partitions • Data properties• Object properties • Restrictions • Union, intersection, and complement• Definitions (equivalent to relations)• Individuals • Other constructs 5. Automatic reasoning6. Modeling exercises7. Summary
Chapter 4: Accessing Ontologies in Python 1. Importing Olwready2. Loading an ontology 3. Imported ontologies4. Listing the content of the ontology 5. Accessing to entities • Individuals • Relations • Classes• Existential restrictions • Properties 6. Searching for entities 7. Huge ontologies and disk cache 8. Namespaces 9. Modifying entity rendering as text 10. Local directory of ontologies 11. Reloading an ontology in the quadstore 12. Example: Creating a dynamic website from an ontology13. Summary
Chapter 5: Creating and Modifying Ontologies in Python 1. Creating an empty ontology 2. Creating classes 3. Creating properties 4. Creating individuals 5. Modifying entities: Relations and existential restrictions6. Creating entities within a namespace7. Renaming entities (refactoring)8. Multiple definitions and forward declarations9. Destroying entities 10. Destroying an ontology11. Saving an ontology12. Importing ontologies 13. Synchronization 14. Example: Populating an ontology from a CSV file15. Summary
Chapter 6: Constructs, Restrictions, Class Properties 1. Creating constructs 2. Accessing constructs parameters 3. Restrictions as class properties 4. Defined classes 5. Example: Creating the ontology of bacteria in Python6. Example: Populating an ontology with defined classes7. Summary
Chapter 7: Automatic Reasoning 1. Disjoints 2. Open-world assumption3. Reasoning in a closed world, or in a local closed world4. Inconsistent classes and inconsistent ontologies5. Restriction and reasoning on numbers and strings 6. SWRL rules 7. Example: An ontology-based decision support system8. Summary
Chapter 8: Annotations, Multilingual Texts and Full Text Search 1. Annotating entities2. Multilingual texts3. Annotating constructs4. Annotating properties and relations 5. Creating new annotation classes6. Ontology metadata 7. Full text search 8. Example: Using DBpedia in Python • Loading DBpedia • A search engine for Dbpedia9. Summary
Chapter 9: Using Medical Terminologies with PyMedTermino and UMLS 1. UMLS 2. Importing terminologies from UMLS 3. Loading terminologies after initial importation 4. Using ICD10 5. Using SNOMED CT6. Using UMLS unified concepts (CUI)7. Transcoding between terminologies8. Manipulating sets of concepts 9. Importing all terminologies in UMLS10. Example: Linking the ontology of bacteria with UMLS11. Example: A multi-terminology browser12. Summary
Chapter 10: Mixing Python and OWL 1. Adding Python methods to OWL classes 2. Associating a Python module to an ontology• Manual import • Automatic import 3. Polymorphism with type inference 4. Introspection 5. Reading restrictions backward 6. Example: using Gene Ontology and managing part-of relations7. Example: A “dating site” for proteins8. Summary
Chapter 11: Working with RDF Triples and Worlds 1. RDF triples2. Manipulating RDF triples with RDFlib 3. Performing SPARQL requests 4. Accessing RDF triples with Owlready5. Interrogating the SQLite3 database directly6. Creating several, isolated, world7. Summary
Annex A: Description logicsAnnex B: Notations for formal ontologiesAnnex C: Reference manual
