Applied Ontology 2018
PHI 598 Registration 24696
An ontology is a structured collection of terms and definitions that is developed with the goal of making data deriving from heterogeneous sources more easily searchable, comparable or combinable. The course will provide an introduction to ontology from an application oriented point of view, including examples in the areas of data science and artificial intelligence. Examples will be drawn from biology and medicine, social science, law, and finance. The course will be of interest not only to philosophers but also to those interested in biomedical informatics and in the computer and information sciences.
Venue: 200G Baldy, UB North Campus
- 1. Arp, Spear and Smith, 2016: Building Ontologies with Basic Formal Ontology, MIT Press, 2016
- 2. Smith, 2003 "Ontology"
- 3. (To be read in advance of August 27 class) Hoehndorf, Schofield & Gkoutos, 2015
- 1 August 27: Introduction to Ontology
- 2 September 3: Labor Day – No class
- 3 September 10: Ontology of Disease
- 4 September 17 Basic Formal Ontology
- 5 September 24: Ontology and Information Engineering (IE) in the Healthcare Domain
- 6 October 1: Big Data and How to Overcome the Problems It Causes
- 7 October 8: Protégé Class
- 8 October 15: Ontological Realism
- 9 October 22: Ontology of Organizations
- 10 October 29: Artificial Intelligence and Machine Learning
- 11 November 5: Building Ontologies: Examples and Worked Exercises
- 12 November 12: Finance Ontology
- 13 November 19: Ontology of Capabilities
- 14 November 26: Presentations of Student Projects 1
- 15 December 3: Presentations of Student Projects 2
- 16 Student Learning Outcomes
- 17 Important dates
- 18 Grading
- 19 Related Policies and Services
- 20 Background Reading and Video Materials
August 27: Introduction to Ontology
- What is an ontology?
- Key elements of an ontology
- What are ontologies useful for?
First class assignment: write a 2-page essay summarizing the key elements of an ontology as identified in the lecture and comparing them to the view of an ontology offered in (Hoehndorf, Schofield & Gkoutos, 2015). Deadline: noon, September 6.
September 3: Labor Day – No class
September 10: Ontology of Disease
- Disease from the clinician’s perspective,
- Ontological approaches to disease,
- The Ontology for General Medical Science
Second class assignment: Summarize in a 2 page essay the issues discussed in pages 16-21 of Haendel et. al., 2018 and describe how the framework offered by Scheuermann, Ceusters and Smith, 2009 might resolve them.
Advance reading (prior to September 17 lecture): Chapters 5 and 6 of Arp, Smith and Spear, 2016
September 17 Basic Formal Ontology
BFO can be reviewed here
Advance reading (prior to September 24 lecture): SW Smith and Koppel, 2014
September 24: Ontology and Information Engineering (IE) in the Healthcare Domain
- Ontology look-alikes
- Use of ontology and look-alikes in biomedical applications
- BFO as benchmark for biomedical IE
Third class assignment: Summarize in a 2-page essay the problems discussed in )(SW Smith and Koppel, 2014) and describe how Basic Formal Ontology can assist in dealing solving them
Advance reading (prior to October 1 lecture): Merelli, et al, 2014
October 1: Big Data and How to Overcome the Problems It Causes
- Definition of 'Big Data'
- Overview of machine learning and other approaches to the exploitation of Big Data
- Role of ontology in Data Science
October 8: Protégé Class
Protégé is the leading open-source ontology editor
This class will be taught by Brian Donohue
Fourth class assignment: Create a simple ontology using Protégé. Deadline: noon, 25 October.
October 15: Ontological Realism
- Conceptual vs. realist approaches to ontology
- Universals and defined classes
- Realism about universals
October 22: Ontology of Organizations
October 29: Artificial Intelligence and Machine Learning
November 5: Building Ontologies: Examples and Worked Exercises
November 12: Finance Ontology
November 19: Ontology of Capabilities
November 26: Presentations of Student Projects 1
December 3: Presentations of Student Projects 2
Student Learning Outcomes
|Program Outcomes/Competencies||Instructional Method(s)||Assessment Method(s)|
|The student will acquire a knowledge of current ontology research in biomedical informatics, data fusion, defense and intelligence||Video lectures and online discussions||Review of submitted content and of participation in class discussions|
|The student will acquire experience in ontology development||Video lectures and critique of successive drafts||Review of results in the form of xsl spreadsheet or Protégé file|
|The student will acquire experience in communicating the results of work on ontology development||Creation of youtube presentation and of associated documentation||Review of results|
|Sep 6||- first class assignment due|
|Sep 24||- second class assignment due|
|Oct 15||- third class assignment due|
|Oct 18||- fourth class assignment due|
|Nov 6||- submit a table of contents and 300 word summary plus draft of associated ppt slides|
|Nov 17||- submit penultimate draft of essay and powerpoint|
|Dec 4||- submit final version of essay and powerpoint|
Grading will be based on two factors:
I: understanding and criticism of the videos presented in classes 1-13
All students are required to ingest the content of all videos and to take an active part in on-line discussions throughout the semester.
II: preparation of a youtube video and associated documentation (including powerpoint slides and essay).
Content and structure of the essay should be discussed with Dr Smith. Where the essay takes the form of the documentation of a specific ontology developed by the student it should include:
- Statement of scope of the ontology
- Summary of existing ontologies in the relevant domain
- Explanation of how your ontology differs from (or incorporates) these ontologies
- Screenshots of parts of the ontology with some examples of important terms and definitions
- Summaries of potential applications of the ontology
Grading Policy: Grading follows standard Graduate School policies. Grades will be weighted according to the following breakdown:
- 26% - video summaries (2% per summary)
- 14% - forum participation
- 20% - youtube video
- 20% - powerpoint slides
- 20% - essay / ontology content
Grade Quality Percentage
|A-||3.67||90.0% - 92.9%|
|B+||3.33||87.0% - 89.9%|
|B||3.00||83.0% - 86.9%|
|B-||2.67||80.0% - 82.9%|
|C+||2.33||77.0% - 79.9%|
|C||2.00||73.0% - 76.9%|
|C-||1.67||70.0% - 72.9%|
|D+||1.33||67.0% - 69.9%|
|D||1.00||60.0% - 66.9%|
|F||0||59.9% or below|
An interim grade of Incomplete (I) may be assigned if the student has not completed all requirements for the course. An interim grade of 'I' shall not be assigned to a student who did not attend the course. The default grade accompanying an interim grade of 'I' shall be 'U' and will be displayed on the UB record as 'IU.' The default Unsatisfactory (U) grade shall become the permanent course grade of record if the 'IU' is not changed through formal notice by the instructor upon the student's completion of the course.
Assignment of an interim 'IU' is at the discretion of the instructor. A grade of 'IU' can be assigned only if successful completion of unfulfilled course requirements can result in a final grade better than the default 'U' grade. The student should have a passing average in the requirements already completed. The instructor shall provide the student specification, in writing, of the requirements to be fulfilled.
The university’s Graduate Incomplete Policy can be found here.
Related Policies and Services
Academic integrity is a fundamental university value. Through the honest completion of academic work, students sustain the integrity of the university while facilitating the university's imperative for the transmission of knowledge and culture based upon the generation of new and innovative ideas. See http://grad.buffalo.edu/Academics/Policies-Procedures/Academic-Integrity.html.
Accessibility resources: If you have any disability which requires reasonable accommodations to enable you to participate in this course, please contact the Office of Accessibility Resources in 60 Capen Hall, 645-2608 and also the instructor of this course during the first week of class. The office will provide you with information and review appropriate arrangements for reasonable accommodations, which can be found on the web here.
Students are expected to attend all lectures. For religious observances, university sanctioned events, athletic commitments and family/work obligations/emergencies, absences may be granted upon request but can have an effect on the finally obtained grade (see grading policy) For course cancellation/emergency planning, see the university website for cancellations/delays due to weather or other unforeseen events (http://emergency.buffalo.edu/campus-weather-alerts.html)
Students are expected to arrive in due time for each class. Some lectures will start with a pre-lecture test to assess the student’s level of preparation for the class. This test contributes to the final grading. Use of cell phones and laptops is allowed for the purposes of the class, but not for private reasons. Phone calls are not allowed.