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PHI 598
PHI 598 Registration [http://www.buffalo.edu/class-schedule?switch=showclass&semester=fall&division=GRAD&dept=PHI&regnum=24696 24696]
 
Partially co-located with BMI508 Biomedical Ontology [http://www.referent-tracking.com/RTU/files/BMI508-2018-syllabus.pdf Syllabus]


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.
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
'''Venue:''' 200G Baldy, UB North Campus
'''Time:''' Mondays, 1:00-3:50pm starting August 27, 2018


'''Faculty:''' [http://ontology.buffalo.edu/smith/ Barry Smith] and [http://www.referent-tracking.com/RTU/ceusters_vita.html Werner Ceusters]
'''Faculty:''' [http://ontology.buffalo.edu/smith/ Barry Smith] and [http://www.referent-tracking.com/RTU/ceusters_vita.html Werner Ceusters]
Line 9: Line 13:
'''Background reading:'''  
'''Background reading:'''  
*1. Arp, Spear and Smith, 2016: ''Building Ontologies with Basic Formal Ontology'', MIT Press, 2016
*1. Arp, Spear and Smith, 2016: ''Building Ontologies with Basic Formal Ontology'', MIT Press, 2016
*2. Please read in advance of August 27 class: [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4652617/ Hoehndorf, Schofield & Gkoutos, 2015]
*2. Smith, 2003 [http://ontology.buffalo.edu/smith/articles/ontology_PIC.pdf "Ontology"]


==August 27: Introduction to Ontology==
==August 27: Introduction to Ontology==
Line 16: Line 20:
:What are ontologies useful for?
:What are ontologies useful for?


Class assignment: write a 2-page essay documenting which of the key elements identified in the lecture are considered (or not considered) in: Hoehndorf, Schofield and Gkoutos, 2015. Deadline: noon, September 6.
[https://buffalo.box.com/s/wmdex6j6xulekx31yc3tju5r9pdzjmk0 Slides]
[https://www.youtube.com/watch?v=9AsRE437e7I Video]
 
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 [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4652617/ Hoehndorf, Schofield & Gkoutos, 2015]). Deadline: noon, September 6.


Advance reading (prior to September 10 lecture): 1. [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041577/ Scheuermann, Ceusters and Smith, 2009]. 2. [https://www.annualreviews.org/doi/pdf/10.1146/annurev-biodatasci-080917-013459 Haendel ''et. al.'', 2018]
Advance reading (prior to September 10 lecture): 1. [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041577/ Scheuermann, Ceusters and Smith, 2009]. 2. [https://www.annualreviews.org/doi/pdf/10.1146/annurev-biodatasci-080917-013459 Haendel ''et. al.'', 2018]
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==September 3: Labor Day – No class==
==September 3: Labor Day – No class==


==September 10: Ontology of Disease
==September 10 Basic Formal Ontology==
 
:Top-level ontologies
:Introduction to BFO
 
BFO can be reviewed [http://www.ontobee.org/ontology/bfo here]
 
[https://buffalo.box.com/s/4nkf3nykjqgb7dbuquc7qiaagsixmxx7 Slides] [https://www.youtube.com/watch?v=9LVfIgBpuaY Video]
 
Advance reading (prior to September 24 lecture): [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3912703/ SW Smith and Koppel, 2014]
 
==September 17: Ontology and Information Engineering in the Healthcare Domain==
 
:Ontology look-alikes
:Use of ontology and look-alikes in biomedical applications
:BFO as benchmark for biomedical Information Engineering (IE)
 
[http://www.referent-tracking.com/RTU/files/BMI508-PHI598-20180917-Ontology-and-Healthcare-IE-covered.pptx Slides]
 
Second class assignment: Summarize in a 2-page essay the problems discussed in ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3912703/ SW Smith and Koppel, 2014]) and describe how Basic Formal Ontology can assist in dealing solving them
 
Advance reading (prior to October 1 lecture): [https://www.hindawi.com/journals/bmri/2014/134023/ Merelli, ''et al'', 2014]
 
==September 24: Ontology of Disease==
 
:Disease from the clinician’s perspective,
:Ontological approaches to disease,
:The [http://www.ontobee.org/ontology/ogms Ontology for General Medical Science]
 
[http://www.referent-tracking.com/RTU/files/BMI508-PHI598-20180924-Ontology-of-Disease.pptx Slides]
 
Third class assignment: Summarize in a 2-page essay the issues discussed in pages 16-21 of [https://www.annualreviews.org/doi/pdf/10.1146/annurev-biodatasci-080917-013459 Haendel ''et. al.'', 2018] and describe how the framework offered by [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041577/ 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
 
==October 1: Disease / Aging / Ontology Building ==
 
Ontology of Disease (Continued)
 
[https://buffalo.box.com/s/e19121ir7g10uvkpmgjp881qu8t6s8rk Slides]
[https://buffalo.box.com/s/pwsqct5xmjlave0ivhhn8c3sborqp2s5 Video]
 
Ontology of Aging
 
[https://buffalo.box.com/s/1pg9hjg8qurqrovtvjfl38nilheyqq4u Slides]
[https://buffalo.box.com/s/0omqle9eq4upir02owjxbyyk18jkdsmh Video]
 
Ontology Building
 
[https://buffalo.box.com/s/w2is3tp3h0ef8yf3hpg9wkfs9brrqn1p Slides] [https://buffalo.box.com/s/hgfmxwdwlq05yptyp93ieq5haakde8zx Video]
 
Reading:
 
:[https://philpapers.org/rec/SCHTAO-29 Toward an Ontological Treatment of Disease and Diagnosis]
 
==October 8: Introduction to Protégé ==
 
[https://protege.stanford.edu/ Protégé] is the leading open-source ontology editor
 
This class taught by [https://www.linkedin.com/in/brian-donohue-72318973/ Brian Donohue]
 
[https://buffalo.box.com/s/pb0bb6tc7dxfbjdtqw4kd64r61flydco Slides]
[https://buffalo.box.com/s/uwy5pxuq96ira873aij43gx7u69emv9b Video]
 
Fourth class assignment: Create a simple ontology using Protégé. Deadline: noon, 25 October.
 
==October 15: Pain / Bruxism / Embryontology ==
 
Ontology of Pain
 
[https://buffalo.box.com/s/p1fn1n0ydvekzu3c5b3fc7q9vbgxh9a4 Slides] [https://buffalo.box.com/s/7jfap1h4mzn6yelve37dzjq0l7fp3jpt Video]
 
Bruxism
 
[https://buffalo.box.com/s/p9t9iuol7p1rtcuvkd2voogboh4vr5uy Slides]
[https://buffalo.box.com/s/7bhyo2l47re85ll6auf53a5xaj1b47f2 Video]
 
Embryontology
 
[https://buffalo.box.com/s/wmdfryxwrj59bb4mbyhwfaj0ez9g10z8 Slides]
[https://buffalo.box.com/s/7bhyo2l47re85ll6auf53a5xaj1b47f2 Video]
 
'''Readings:'''
:[http://ontology.buffalo.edu/smith/articles/pain.pdf "Ontology of Pain"]
:[http://ontology.buffalo.edu/smith/articles/embryontology.pdf "16 Days"]
 
Fifth class assignment: Create a plan for your presentation on December 3
 
==October 22: Joint Doctrine Ontology / Building an Ethical Warfighter / Terrorism==
 
Joint Doctrine Ontology (JDO)
 
[https://buffalo.box.com/s/6jst6ri1hxljzz23gih5bench9ibkozh Slides] [https://www.youtube.com/watch?v=rqrVmlHOqC4 Video]
 
Building an Ethical Warfighter
 
[https://buffalo.box.com/s/vsih0bbo3uj9t9if79yw8phlplbds2pi Slides] [https://www.youtube.com/watch?v=Sj_nKsGR-54 Video]
 
Ontology of Terrorism
 
[https://buffalo.box.com/s/edi8jqz4voaid8wcw21n4q9fb0n8xhrm Slides] [https://www.youtube.com/watch?v=YeMWBt-rH8s Video]
 
'''Readings''':
:[http://www.jcs.mil/Portals/36/Documents/Doctrine/pubs/dictionary.pdf Department of Defense Dictionary of Military and Associated Terms]
:[http://stids.c4i.gmu.edu/papers/STIDS_2015_T01_Morosoff_etal.pdf P. Morossof et al., "Joint Doctrine Ontology: A Benchmark for Military Information Systems Interoperability" (2015)]
:[https://www.researchgate.net/publication/328145335_From_Affective_Science_to_Psychiatric_Disorder_Ontology_as_a_Semantic_Bridge R. R. Larsen and J. Hastings, "From Affective Science to Psychiatric Disorder: Ontology as a Semantic Bridge" (2018)]
 
==October 29: Top-Level Ontologies / The Six-Category Ontology / Truth and Maps==
 
Top-Level Ontologies
[https://buffalo.box.com/s/g0wvvijd47yxfcklxfoybkdzc1vaj0tn Slides] [https://www.youtube.com/watch?v=P0gV0nCB0ng Video]


Class assignment: write a 2-page essay discussing the extent on which the framework offered by Scheuermann, Ceusters and Smith, 2009 can (or can not) solve the issues discussed on pp. 16-21 of Haendel ''et. al.'', 2018. Deadline: noon, September 24
The Six-Category Ontology


Big Data and How to Overcome the Problems It Causes==
[https://buffalo.box.com/s/gh9x7s4eu3qgpeg0fu2jf7gqor8t4zjh Slides] [https://www.youtube.com/watch?v=pRY5AFTEWrA Video]


:Definition of 'Big Data'
Truth and the Ontology of Maps
:Overview of machine learning and other approaches to the exploitation of Big Data
 
[https://buffalo.box.com/s/voymfa5vgmu2mc6721flo69l51ka5131 Slides] [https://www.youtube.com/watch?v=Jqqq7eBnZvE Video]
 
'''Readings:'''
:[http://www.inf.ed.ac.uk/teaching/courses/kmm/PDF/L7-DOLCE.pdf DOLCE: An Upper-Level Ontology]
:[http://www.adampease.org/OP/ SUMO Suggested Upper Merged Ontology]
:http://ncorwiki.buffalo.edu/index.php/Basic_Formal_Ontology_2.0 Basic Formal Ontology]
 
==November 5: From Speech Acts to Document Acts / Social Agency / Deontics ==
 
From speech acts to document acts
 
[https://buffalo.box.com/s/2iueose1ii7l20bu50lmrofvh3l41c7x Slides] [https://www.youtube.com/watch?v=5chInYVVypI Video]
 
Massively planned social agency
 
[https://buffalo.box.com/s/fcy56onfs5omtoqe7k3x95q8otkcguhs Slides] [https://www.youtube.com/watch?v=n3V8UWby2Gw Video]
 
Deontic entities
 
[https://buffalo.box.com/s/xrpf0b84619qcxuvcdi08ri3ufhh9zp1 Slides] [https://www.youtube.com/watch?v=g7vplac5JP0 Video]
 
==November 12: Artificial Intelligence, Deep Learning, Machine Learning / Money  ==
 
:Overview of machine learning and other approaches to the exploitation of Big Data (presented by [https://krkeane.github.io/about/ Kevin Keane])
:Role of ontology in Data Science
:Role of ontology in Data Science
:Ontology of money
[https://buffalo.box.com/s/4t7ilrkivp5j3po63fiyklv1uo0cxdwq Slides] [https://www.youtube.com/watch?v=dHo-Tn_v8xM Video]
'''Readings''':
:[http://ontology.buffalo.edu/smith/articles/searle.pdf Barry Smith and John Searle (2003) "The Construction of Social Reality: An Exchange"]
:[http://www.cs.cmu.edu/~tom/mlbook/keyIdeas.pdf Tom Mitchell, "Key Ideas in Machine Learning"]
:[https://courses.csail.mit.edu/18.337/2015/docs/50YearsDataScience.pdf David Donoho, "50 years of Data Science"]
:[http://arxiv.org/abs/1801.00631 G. Marcus (2018), "Deep Learning: A Critical Appraisal"]
==November 19: The Ontology of the Eruv ==
The Ontology of the Eruv
[https://buffalo.box.com/s/ovo1meikzduv4psbes8mkmqb3qvoce7e Slides] [https://www.youtube.com/watch?v=hCJFGljz4PQ Video]
Reading:
:[https://philpapers.org/rec/KUMTOO The Ontology of Processes and Functions]
:[https://philpapers.org/archive/SMIOPA-3.pdf The Ontology of the Eruv]
==November 26: Why computer science needs philosophy / Why I am not a Philosopher ==
Why computer science needs philosophy
[https://buffalo.box.com/s/ysavl3d65vyxke9tnt78u9jb7d3mk3pf Slides] [https://www.youtube.com/watch?v=0yfhUt1LrIo Video]
Why I am not a philosopher
[https://buffalo.box.com/s/y74umhxrfod6jr5zhh9g659pgea2weld Slides] [https://youtu.be/e5zjZnbi-ZA Video]
==December 3: Student Projects ==
1:05pm Botan Dolun: The Metaphysics of States
[https://buffalo.box.com/s/rl2mo4l5uq43g6b2ypj9ka5gq3vyijuo Slides]
1:20pm Angie Li: Ontology Representing Human Artificial Reproductive Technologies


[https://buffalo.box.com/s/s42d2e2ped7omg9u9964rx14v742plqy Slides]


Advance reading (prior to September 17 lecture): Chapters 5 and 6 of Arp, Smith and Spear, 2016
1:35pm Zihe Luo: The Music Ontology
 
[https://buffalo.box.com/s/1n5o83lwwep7k7p8t29584lci08gsgua Slides]
 
1:50pm Jinwei Hu: Patient Conditions: Referent Tracking and Prognostic Terms
 
[https://buffalo.box.com/s/036e757j35vmyv6lnrd9duei47v6w4qr Slides]
 
2:05pm Alexander Anderson:  Quantum Realism
 
[https://buffalo.box.com/s/q7l143q7pp0vrww3cm6e7u6ikgusd7qj Slides]
 
2:20pm Shyamashree Srinha: Opioid Use Disorder in the
Light of Ontology
 
[https://buffalo.box.com/s/392qu8r1zksf5ezww8zr1aejxa56log9 Slides]
 
2:40pm William Mangione: The Drug Repurposing Ontology
 
[https://buffalo.box.com/s/xt1ho7gqfnshm2vg2txxgbs4ogxrx7lc Slides]
 
3:00pm Jonathan Vajda: On the Relation Between a Biospecimen and its Source
 
[https://buffalo.box.com/s/5f9854k2zdu1qv8yq7vyg6a933d4ihrq Slides]
 
3:20pm Eric Merrell: Ontology of Fictional Entities
 
[https://buffalo.box.com/s/g9hl0xcp934pe52mzy1m63b2tp7paei1 Slides]
 
3:35pm Arlen Brickman: Defining Cancer
 
== '''Student Learning Outcomes''' ==
         
{| class="wikitable"
|-
! 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
|}
 
=='''Important dates'''==
{|
|  Sep 6 || - first class assignment due
|-
|  Sep 24 || - second class assignment due
|-
|  Oct 15 || - third class assignment due
|-
|  Oct 18 || - fourth class assignment due
|-
|  Oct 25 || - Protege 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'''==
 
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 [http://grad.buffalo.edu/Academics/Policies-Procedures/Grading-Procedures.html Graduate School policies]. Grades will be weighted according to the following breakdown:
 
Weighting Assignment
:26%    - video summaries (2% per summary)
:14%    - forum participation
:20%    - youtube video
:20%    - powerpoint slides
:20%    - essay / ontology content
 
'''Final Grades'''
 
Grade Quality Percentage
{|
|  A || 4.0 || 93.0% -100.00%
|-
| 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 [http://grad.buffalo.edu/study/progress/policylibrary.a-to-z.html#iugrade 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 [http://www.buffalo.edu/studentlife/who-we-are/departments/accessibility.html here].
 
'''Attendance Policy'''
 
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)
 
'''Classroom Decorum'''


==September 17 Basic Formal Ontology==
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.


== '''Background Reading and Video Materials''' ==


Advance reading (prior to September 24 lecture): [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3912703/ SW Smith and Koppel, 2014]
*[http://ontology.buffalo.edu/smith/articles/ontologies.htm Ontology: An Introduction]


==September 24: Ontology and Information Engineering in the Healthcare Domain==
*[https://wiki.csc.calpoly.edu/OntologyTutorial/wiki/IntroductionToOntologiesWithProtege Protégé Tutorial]


*[http://protegewiki.stanford.edu/wiki/Protege4GettingStarted Getting Started with Protege 4].


*[http://owl.cs.manchester.ac.uk/tutorials/protegeowltutorial Matthew Horridge's Protege-OWL Tutorial].


*[http://militaryontology.org Military Ontology]


==October 1: ==
*[https://www.youtube.com/user/hxo3nql Streaming video presentations and training courses in ontology]
==October 8: Protege Class (Brian Dononue)==
==October 15: Ontological Realism ==
:Reading: https://www.ncbi.nlm.nih.gov/pubmed/21431244
==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==

Latest revision as of 17:27, 28 December 2018

PHI 598 Registration 24696

Partially co-located with BMI508 Biomedical Ontology Syllabus

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

Time: Mondays, 1:00-3:50pm starting August 27, 2018

Faculty: Barry Smith and Werner Ceusters

Background reading:

  • 1. Arp, Spear and Smith, 2016: Building Ontologies with Basic Formal Ontology, MIT Press, 2016
  • 2. Smith, 2003 "Ontology"

August 27: Introduction to Ontology

What is an ontology?
Key elements of an ontology
What are ontologies useful for?

Slides Video

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.

Advance reading (prior to September 10 lecture): 1. Scheuermann, Ceusters and Smith, 2009. 2. Haendel et. al., 2018

September 3: Labor Day – No class

September 10 Basic Formal Ontology

Top-level ontologies
Introduction to BFO

BFO can be reviewed here

Slides Video

Advance reading (prior to September 24 lecture): SW Smith and Koppel, 2014

September 17: Ontology and Information Engineering in the Healthcare Domain

Ontology look-alikes
Use of ontology and look-alikes in biomedical applications
BFO as benchmark for biomedical Information Engineering (IE)

Slides

Second 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

September 24: Ontology of Disease

Disease from the clinician’s perspective,
Ontological approaches to disease,
The Ontology for General Medical Science

Slides

Third 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

October 1: Disease / Aging / Ontology Building

Ontology of Disease (Continued)

Slides Video

Ontology of Aging

Slides Video

Ontology Building

Slides Video

Reading:

Toward an Ontological Treatment of Disease and Diagnosis

October 8: Introduction to Protégé

Protégé is the leading open-source ontology editor

This class taught by Brian Donohue

Slides Video

Fourth class assignment: Create a simple ontology using Protégé. Deadline: noon, 25 October.

October 15: Pain / Bruxism / Embryontology

Ontology of Pain

Slides Video

Bruxism

Slides Video

Embryontology

Slides Video

Readings:

"Ontology of Pain"
"16 Days"

Fifth class assignment: Create a plan for your presentation on December 3

October 22: Joint Doctrine Ontology / Building an Ethical Warfighter / Terrorism

Joint Doctrine Ontology (JDO)

Slides Video

Building an Ethical Warfighter

Slides Video

Ontology of Terrorism

Slides Video

Readings:

Department of Defense Dictionary of Military and Associated Terms
P. Morossof et al., "Joint Doctrine Ontology: A Benchmark for Military Information Systems Interoperability" (2015)
R. R. Larsen and J. Hastings, "From Affective Science to Psychiatric Disorder: Ontology as a Semantic Bridge" (2018)

October 29: Top-Level Ontologies / The Six-Category Ontology / Truth and Maps

Top-Level Ontologies

Slides Video

The Six-Category Ontology

Slides Video

Truth and the Ontology of Maps

Slides Video

Readings:

DOLCE: An Upper-Level Ontology
SUMO Suggested Upper Merged Ontology
http://ncorwiki.buffalo.edu/index.php/Basic_Formal_Ontology_2.0 Basic Formal Ontology]

November 5: From Speech Acts to Document Acts / Social Agency / Deontics

From speech acts to document acts

Slides Video

Massively planned social agency

Slides Video

Deontic entities

Slides Video

November 12: Artificial Intelligence, Deep Learning, Machine Learning / Money

Overview of machine learning and other approaches to the exploitation of Big Data (presented by Kevin Keane)
Role of ontology in Data Science
Ontology of money

Slides Video

Readings:

Barry Smith and John Searle (2003) "The Construction of Social Reality: An Exchange"
Tom Mitchell, "Key Ideas in Machine Learning"
David Donoho, "50 years of Data Science"
G. Marcus (2018), "Deep Learning: A Critical Appraisal"

November 19: The Ontology of the Eruv

The Ontology of the Eruv

Slides Video

Reading:

The Ontology of Processes and Functions
The Ontology of the Eruv

November 26: Why computer science needs philosophy / Why I am not a Philosopher

Why computer science needs philosophy

Slides Video

Why I am not a philosopher

Slides Video

December 3: Student Projects

1:05pm Botan Dolun: The Metaphysics of States

Slides

1:20pm Angie Li: Ontology Representing Human Artificial Reproductive Technologies

Slides

1:35pm Zihe Luo: The Music Ontology

Slides

1:50pm Jinwei Hu: Patient Conditions: Referent Tracking and Prognostic Terms

Slides

2:05pm Alexander Anderson: Quantum Realism

Slides

2:20pm Shyamashree Srinha: Opioid Use Disorder in the Light of Ontology

Slides

2:40pm William Mangione: The Drug Repurposing Ontology

Slides

3:00pm Jonathan Vajda: On the Relation Between a Biospecimen and its Source

Slides

3:20pm Eric Merrell: Ontology of Fictional Entities

Slides

3:35pm Arlen Brickman: Defining Cancer

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

Important dates

Sep 6 - first class assignment due
Sep 24 - second class assignment due
Oct 15 - third class assignment due
Oct 18 - fourth class assignment due
Oct 25 - Protege 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

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:

Weighting Assignment

26% - video summaries (2% per summary)
14% - forum participation
20% - youtube video
20% - powerpoint slides
20% - essay / ontology content

Final Grades

Grade Quality Percentage

A 4.0 93.0% -100.00%
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.

Attendance Policy

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)

Classroom Decorum

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.

Background Reading and Video Materials

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