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Ontologies with Python Lamy Jean-Baptiste

Ontologies with Python By Lamy Jean-Baptiste

Ontologies with Python by Lamy Jean-Baptiste

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Ontologies with Python Summary

Ontologies with Python: Programming OWL 2.0 Ontologies with Python and Owlready2 by Lamy Jean-Baptiste

Use ontologies in Python, with the Owlready2 module developed for ontology-oriented programming. You will start with an introduction and refresher on Python and OWL ontologies. Then, you will dive straight into how to access, create, and modify ontologies in Python. Next, you will move on to an overview of semantic constructs and class properties followed by how to perform automatic reasoning. You will also learn about annotations, multilingual texts, and how to add Python methods to OWL classes and ontologies. Using medical terminologies as well as direct access to RDF triples is also covered.

Python is one of the most used programming languages, especially in the biomedical field, and formal ontologies are also widely used. However, there are limited resources for the use of ontologies in Python. Owlready2, downloaded more than 60,000 times, is a response to this problem, and this book is the first one on the topic of using ontologies with Python.

What You Will Learn

  • Use Owlready2 to access and modify OWL ontologies in Python
  • Publish ontologies on dynamic websites
  • Perform automatic reasoning in Python
  • Use well-known ontologies, including DBpedia and Gene Ontology, and terminological resources, such as UMLS (Unified Medical Language System)
  • Integrate Python methods in OWL ontologies

Who Is This Book For

Beginner to experienced readers from biomedical sciences and artificial intelligence fields would find the book useful.

About Lamy Jean-Baptiste

Lamy Jean-Baptiste is a senior lecturer at Paris 13 University and a member of the LIMICS, a research lab focused on biomedical informatics. He is also the developer of the Owlready2 Python module that allows access to OWL ontologies. He has developed many research prototypes, and one of them (VCM iconic medical language) has been patented in the US, with three licenses sold to industrial partners.

Lamy speaks regularly at artificial intelligence and medical informatics conferences, has written over 50 journal papers, and is a moderator on the Owlready forum on Nabbles. He was awarded the best paper award at MEDINFO 2019, the largest international conference in medical informatics.

Table of Contents

Chapter 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 Protege 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

Additional information

NLS9781484265512
9781484265512
1484265513
Ontologies with Python: Programming OWL 2.0 Ontologies with Python and Owlready2 by Lamy Jean-Baptiste
Lamy Jean-Baptiste
New
Paperback
APress
2020-12-18
344
N/A
Book picture is for illustrative purposes only, actual binding, cover or edition may vary.
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