Applied Ontology, Spring 2022: Difference between revisions

Latest revision as of 18:17, 10 May 2022

Title: PHI 637 Applied Ontology, Spring 2022

Faculty: Barry Smith

Registration: Class #24730. Non-UB persons should go to this page

Course Structure: This will be a graduate seminar taught primarily online and asynchronously. The course can be taken in either a 2- or a 3-credit hour version. All students are required to

1. prepare a simple ontology file in Protege on a topic of your choice

2. follow the videos released at 1pm on Monday afternoon of each week

3. create 3 questions each week and post these questions to the class listserv; the questions should identify issues relevant to each week's videos but not answered in those videos

4. contribute to the class listserv discussions provoked by these questions

Students taking the class for 2 credits must in addition:

1 create a paper of at least 1,000 words on a topic relevant to the course, topic to be discussed with Dr Smith

Students taking the class for 3 credits must in addition:

1. create successive drafts of a paper of at least 3,000 words on a topic relevant to the course, topic and drafts to be discussed with Dr Smith

2. create a powerpoint slide summarizing the main theses of your paper

3. present the powerpoint slides in the final class session

Course Description: An ontology is a structured controlled vocabulary used primarily for tagging data in a way that will allow the data to be shared between different communities. The course will provide an introduction to ontology from an application oriented point of view, focusing on best practices for the development and use of ontologies, and providing plenty of examples. The course will be open to all students with an undergraduate degree. No prior knowledge of ontologies is required.

Schedule The link to the course video for any given week will be provided at 9am on the corresponding Monday (as listed below). Students are required to watch the video within 48 hours of this posting. Class participants are required to post to the class email forum questions, responses and discussion comments relating to the video from the relevant week.

Students should familiarize themselves with the Protege software tool, which can be downloaded from here.

Tutorials and other supporting material can be found here. Other potentially useful tutorials can be found on youtube, including:

@@ Line 1: / Line 1: @@
-'''Title:''' PHI 549 [[Applied Ontology, Spring 2022]]
+'''Title:''' PHI 637 [[Applied Ontology, Spring 2022]]
 '''Faculty: Barry Smith'''
-'''Registration:''' [http://www.buffalo.edu/cas/philosophy/grad-study/grad_courses/springcourses_grad.html#title_0 Class# 24197]. Registration details for off-campus students are provided under Part Time/Graduate [http://studentaccounts.buffalo.edu/tuition/spring.php here].
+'''Registration:''' [http://www.buffalo.edu/class-schedule?switch=showclass&semester=spring&division=GRAD&dept=PHI&regnum=24730 Class #24730]. Non-UB persons should go to [http://www.buffalo.edu/studentaccounts/tuition-and-fees/spring.non-resident-online.html this page]
-'''Course Structure:''' This will be a two credit hour '''on-line''' graduate seminar. It will be taught through the medium of a series of 2-hour long videos incorporating presentation of powerpoint slides and question-answer sessions. Links to videos will be distributed according to the schedule below. The final session will be structured around youtube videos created by the students in the class.
+'''Course Structure:''' This will be a graduate seminar taught primarily online and asynchronously. The course can be taken in either a 2- or a 3-credit hour version. All students are required to
+:1. prepare a simple ontology file in Protege on a topic of your choice
+:2. follow the videos released at 1pm on Monday afternoon of each week
+:3. create 3 questions each week and post these questions to the class listserv; the questions should identify issues relevant to each week's videos but not answered in those videos
+:4. contribute to the class listserv discussions provoked by these questions
-'''Course Description:''' An ontology is a structured collection of terms used to tag data with the goal of making data deriving from heterogeneous sources more easily searchable, comparable or combinable. Ontologies allow information to be shared across communities of scientists with different sorts of expertise. The Gene Ontology, for example, allows researchers on aging to use data from cell biology, yeast biology, cancer biology, genetics, and gerontology, because all of these disciplines create data that are tagged using Gene Ontology terms. The course will provide an introduction to ontology from an application oriented point of view, focusing on the best practices for ontology development and on the development of plug-and-play ontology modules for re-use in different areas. Examples will be drawn primarily from biology and medicine, but no expertise in these disciplines is presupposed.
+'''Students taking the class for 2 credits''' must in addition:
+:1 create a paper of at least 1,000 words on a topic relevant to the course, topic to be discussed with Dr Smith
+'''Students taking the class for 3 credits''' must in addition:
+:1. create successive drafts of a paper of at least 3,000 words on a topic relevant to the course, topic and drafts to be discussed with Dr Smith
+:2. create a powerpoint slide summarizing the main theses of your paper
+:3. present the powerpoint slides in the final class session
+'''Course Description:''' An ontology is a structured controlled vocabulary used primarily for tagging data in a way that will allow the data to be shared between different communities. The course will provide an introduction to ontology from an application oriented point of view, focusing on best practices for the development and use of ontologies, and providing plenty of examples. The course will be open to all students with an undergraduate degree. No prior knowledge of ontologies is required.
 '''Schedule'''
-The link to the course video for any given week will be provided at 9am on the corresponding Sunday (as listed below). Students are required to watch the video within 48 hours of this posting. Class participants are required to post to the class email forum questions, responses and discussion comments relating to the video from the relevant week.
+The link to the course video for any given week will be provided at 9am on the corresponding Monday (as listed below). Students are required to watch the video within 48 hours of this posting. Class participants are required to post to the class email forum questions, responses and discussion comments relating to the video from the relevant week.
+----
+Students should familiarize themselves with the Protege software tool, which can be downloaded from [https://protege.stanford.edu/ here].
+Tutorials and other supporting material can be found [https://protege.stanford.edu/support.php#documentationSupport here]. Other potentially useful tutorials can be found on youtube, including:
+:[https://www.youtube.com/watch?v=akz0Me7Mdmg&list=PLNBLqX5LhhweENtCIaqRZxKtOLFADKf2O Idris -- very short]
+:[https://www.youtube.com/playlist?list=PLea0WJq13cnAfCC0azrCyquCN_tPelJN1 Sadawi]
+:[https://www.youtube.com/watch?v=CduRWyyL3q8&list=PLNohRKRAHaszTV3puqFM9yXDXnEqjS6Fd&index=1 AI & DS]
 ----
 ==January 31: Introduction to Ontology==
+:[https://buffalo.box.com/s/x33dxkrnidtj0oy5vd031ynggdhme3pz Video]
+:[http://ontology.buffalo.edu/smith/courses09/1_Aristotle.ppt Slides]
+:*A brief history of ontology
+:*Semantically enhanced publishing
+:*GO: The most successful ontology thus far
+:*Aristotle's Metaphysics and Categories
+:*The Ontological Square
+:*Granular partitions
+:*Aristotle vs. Kant
+'''The Ontology of Social Reality'''
+:[https://buffalo.box.com/s/lp4fvsx8gcu1bq1o2kiiozm2yx1osxdl Video]
+:[https://buffalo.box.com/shared/static/5y1o905rciabpl12sda4xut6jn56cspk.ppt Slides]
+:*Speech acts
+:*The money in your bank account
+:*War and chess
+:*Debts
+:*Institutions
+:*Searle's naturalism and its problems
+:*Objects vs. representations
+:*Hernando de Soto and The Mystery of Capital
+:*Ontology of the credit crunch
 ----
@@ Line 20: / Line 65: @@
 ==February 7: Introduction to Applied Ontology==
-----
+The first part of a series presented in the University at Buffalo in January 2018:
+'''Introduction to Ontology for Systems Engineers''' (first part of a series presented in the University at Buffalo in January 2018):
+:[https://www.youtube.com/watch?v=QGmwIWmyJeg Video]
+:[https://buffalo.box.com/s/3ln2y4iwcfhdikvn1xl514qtqx07qopl Slides]
+NAVAIR, NAVSEA and SPAWAR, the three Navy Systems Commands, initiated a [https://web.archive.org/web/20180702211811/https://www.navy.mil/submit/display.asp?story_id=106184 Systems Engineering Transformation (SET)] designed to introduce model-based systems engineering into all aspects of their work. Given the extremely broad scope of this project the immense number and complexity of models to be generated  experiments were made to explore the use ontology as a means of enhancing consistency and discoverability of models and their contents.
+On September 19, 2018 a meeting of the Navy SYSCOMs on the proposed ontology was held in Washington DC, at which Barry Smith delivered two lectures as follows:
+: '''Three ways ontologies fail – with lessons learned for the Navy Systems Engineering Transformation'''
+:[https://www.youtube.com/watch?v=vYr5oB1O6ig Video]
+:[https://buffalo.box.com/s/2hoet9ko03ylaz2o7nrhbl6fj15a4qm8 Slides]
+: '''Ontology for Product Lifecycle Management, or: how to use ontologies to build and fly a plane'''
+:[https://www.youtube.com/watch?v=9s3NCa8sb2w Video]
+:[https://buffalo.box.com/s/k1ak0x1kvqqvp9diqspt4x5t0cxxyjbt Slides]
 ==February 14: Ontology and Artificial Intelligence==
+Ontology of Language, Ontology of Terrorism, Ontology of Obligations
+[https://www.youtube.com/watch?v=G4lg1_-XpiE Video]
+Driverless Philosophy
+:[https://buffalo.box.com/v/Driverless-Philosophy Slides]
+:[https://www.youtube.com/watch?v=29GE_p5GEtY Video]
 ----
 ==Feb 21: Towards a Standard Upper Level Ontology==
+ISO/IEC 21838 Top-Level Ontology
+:[https://buffalo.box.com/v/ontobras-keynote Slides]
+:[https://www.youtube.com/watch?v=aux_zcK7XSI Video]
+Since this video was created both parts 1 and 2 have been approved through the ISO process. Background material can be found [http://ncorwiki.buffalo.edu/index.php/BFO_2020 here]
+Reading: ''[https://buffalo.app.box.com/file/909458641121?s=2klq7ec220w8uapwd0lq3419l017iq9z Building Ontologies with Basic Formal Ontology]''
+----
+==Feb 24: Face-to-Face Question-and-Answer Session==
+[https://buffalo.box.com/v/Applied-Ontology-QandA-1 Video]
+----
+==Feb 28: Basic Formal Ontology ==
+'''BFO Tutorial'''
+:[https://buffalo.box.com/s/vxuua68fmrspe8blozqav7zu4ezes4cw Slides]
+:[https://www.youtube.com/watch?v=VYDe09TOw2M Video Part 1]
+:[https://www.youtube.com/watch?v=wh_KZGXc1Es Video Part 2]
+'''Realizable Entities in Basic Formal Ontology'''
+:[https://buffalo.box.com/v/on-realizables Slides]
+:[https://www.youtube.com/watch?v=PJaEYdF9ikE Video]
+'''Temporalized Relations'''
+:[https://buffalo.box.com/v/Temporalized-Relations Slides]
+:[https://www.youtube.com/watch?v=fkkWkTIxrNQ Video]
+'''Ontology as Product-Service System'''
+:[https://buffalo.box.com/v/ontology-pss Slides]
+:[https://www.youtube.com/watch?v=XTVR7k63_VA Video]
+Reading: ''[https://buffalo.app.box.com/file/909458641121?s=2klq7ec220w8uapwd0lq3419l017iq9z Building Ontologies with Basic Formal Ontology]''
 ----
-==Feb 28: Simple Protege Introduction==
+==Mar 7: Drill==
+:3-credit students submit draft title and abstract of essay
+'''Joint Doctrine Ontology
+:[https://buffalo.box.com/s/6jst6ri1hxljzz23gih5bench9ibkozh Slides]
+:[https://www.youtube.com/watch?v=rqrVmlHOqC4&list=PLyngZgIl3WTi9JJppdtBm6HBtNfbOKqbc&index=1 Video]
+'''Building an Ethical Warfighter
+:[https://buffalo.box.com/v/Building-ethical-warfighter Slides]
+:[https://www.youtube.com/watch?v=Sj_nKsGR-54&list=PLyngZgIl3WTi9JJppdtBm6HBtNfbOKqbc&index=2 Video]
+:(From the [http://ncorwiki.buffalo.edu/index.php/Symposium_on_Military_Codes_of_Ethics Symposium on Military Codes of Ethics], held in Buffalo, November 2015)
+'''Ontology of Terrorism
+:[https://www.youtube.com/watch?v=YeMWBt-rH8s&list=PLyngZgIl3WTi9JJppdtBm6HBtNfbOKqbc&index=3]
+:[https://buffalo.box.com/s/edi8jqz4voaid8wcw21n4q9fb0n8xhrm Slides]
+:(This is a shorter version of the material presented on February 14.)
+'''Massively Planned Social Agency
+:[https://buffalo.app.box.com/s/fcy56onfs5omtoqe7k3x95q8otkcguhs Slides]
+:[https://www.youtube.com/watch?v=n3V8UWby2Gw&list=PLyngZgIl3WTi9JJppdtBm6HBtNfbOKqbc&index=4 Video]
+'''Command and Control
+:[https://buffalo.box.com/v/Command-and-Control Slides]
+:[https://www.youtube.com/watch?v=U8LTHhpF4Wk&list=PLyngZgIl3WTi9JJppdtBm6HBtNfbOKqbc&index=8 Video]
+:(Contains material from the Joint Doctrine Ontology talk above)
 ----
+==Mar 10: Face-to-Face Question-and-Answer Session==
-==Mar 7: Ontology and Referent Tracking==
+In 141 Park Hall from 9am to 10:30am
+:[https://buffalo.box.com/v/Applied-Ontology-Q-A-2 Slides]
+:[https://buffalo.box.com/v/Applied-Ontology-QandA-2 Audio]
 ----
-==Mar 14: Basic Formal Ontology==
+==Mar 14: Ontology of Philosophy==
+The Future of the History of Philosophy
+:[https://buffalo.box.com/v/Future-of-History Slides]
+:[https://www.youtube.com/watch?v=YkYlY2jnRxc&list=PLyngZgIl3WTgZVwgwLUGWMDram5v7rUjk Video]
 ----
 :Mar 21 Spring Recess
-==Mar 28 Basic Formal Ontology (Continued)==
+==Mar 28 Applied Ontology in Geospatial Science==
+Environments Inside and Outside the Organism
+:[https://buffalo.box.com/v/Environments-Organism Slides]
+:[https://www.youtube.com/watch?v=gxihMdMiV0Y&list=PLyngZgIl3WTgH8HNXU4HzjDDxqVl_w0X9 Video]
+Making Space
+:[https://buffalo.box.com/v/Making-Space Slides]
+:[https://www.youtube.com/watch?v=JWtR-UpLhjM Video]
+The Ontology of the Eruv
+:[https://buffalo.box.com/v/Ontology-of-the-Eruv Slides]
+:[https://www.youtube.com/watch?v=hCJFGljz4PQ Video]
+Truth and the Ontology of Maps
+:[https://buffalo.box.com/v/Truth-and-Maps Slides]
+:[https://www.youtube.com/watch?v=Jqqq7eBnZvE Video]
 ==April 4: Ontology of Military Domains==
+Colonel W. Mandrick (UB Ontology PhD) on Military and Intelligence Ontologies
+:[https://www.youtube.com/watch?v=8MlxZtLnshQ Video]
+Will WW3 Be Fought on the Internet?
+:[https://buffalo.app.box.com/v/Next-War-On-Internet Slides]
+:[https://www.youtube.com/watch?v=KVcIud4I7Ok Video]
+Commanding and Other Social Acts
+:[https://buffalo.box.com/v/Command-and-Other-Social-Acts Slides]
+:[https://www.youtube.com/watch?v=tHap_q-dUKk Video]
+:3-credit students submit short draft version of essay
 ==Apr 11: Ontology and Intelligence Analysis==
-==Apr 18: The Ontology of Social Reality ==
+Defining Intelligence
+:[https://www.youtube.com/watch?v=0giPMMoKR9s Video]
+:[https://buffalo.box.com/v/Defining-intelligence Slides]
+Introduction to the Information Artifact Ontology
+:[http://ncor.buffalo.edu/2013/STIDS/2-BS-IAO.pptx Video]
+:[http://ncor.buffalo.edu/2013/STIDS/Video-1.mp4 Slides]
+==Apr 14: Face-to-Face Q&A Meeting==
+am: 141 Park Hall
+[https://buffalo.box.com/v/Face-to-face-April-14 Video]
+==Apr 18: Ontology of Space==
+'''Ontologies for Space and Ground Systems'''
+:[https://buffalo.app.box.com/v/Space-Ontology-GSAW-2020 Slides]
+:[https://www.youtube.com/watch?v=x3ugXHOyLLw Video]
+==Apr 25: Ontology of Biomedicine ==
+Principles for Building Biomedical Ontologies
+:[https://buffalo.box.com/v/Principles-of-Bio-Ontologies Slides]
+:[https://www.youtube.com/watch?v=2zRXopVZAAg Video]
+The Glory and Misery of Electronic Health Records
+:[https://www.youtube.com/watch?v=gc5a0LaXaBo Video]
+Infectious Disease Ontology and Covid 19
+:[https://buffalo.app.box.com/v/ID0-COVID-19 Slides]
+:[https://www.youtube.com/watch?v=kM3eZHzMGtg Video]
+Mar 2, 2019
+In Defense of the Container Theory: A Contribution to the Metaphysics of Pregnancy
+:[https://buffalo.box.com/shared/static/tq3f3zl51kuqsspzkqma4xh3t2edhlqc.pptx Slides]
+:[https://www.youtube.com/watch?v=_kcTsgW46xc Video]
+==May 2: Artificial Intelligence ==
+The Machine Will
+:[https://buffalo.box.com/v/The-Machine-Will Slides]
+:[https://www.youtube.com/watch?v=6e2_LtRcb1U Video]
-==Apr 25: Ontology of Military Domains==
+AI and the Ontology of Complex Systems
+:[https://buffalo.box.com/v/AI-and-Systems-Toronto Slides]
+:[https://www.youtube.com/watch?app=desktop&v=HhyE5GpTlcQ Video]
-==May2: Ontology of Biology ==
+==May 5: Q&A Session==
-==May 9 Student video presentations==
+[https://buffalo.box.com/v/Applied-Ontology-QA-May5 Video]
+==May 12: 9:00-10:30am: Student video presentations==
+To take place in 141 Park Hall.
+:00  Cameron More: '''Towards an Ontology of Sports'''
+:20 Peihong (Karl) Xie: '''Automobile Rental Ontology'''
+:40 Robert Krieter: '''BFO and Substantiating a Top-Level Ontology'''
+:00 Ali Hasanzadeh: '''Beer Ontology'''
 ==Background Materials==
-'''Text:''' Robert Arp, Barry Smith and Andrew Spear, [https://mitpress.mit.edu/index.php?q=books/building-ontologies-basic-formal-ontology Building Ontologies with Basic Formal Ontology], Cambridge, MA: MIT Press, August 2015
+'''Text:''' Robert Arp, Barry Smith and Andrew Spear, [https://buffalo.box.com/s/2klq7ec220w8uapwd0lq3419l017iq9z ''Building Ontologies with Basic Formal Ontology]'', Cambridge, MA: MIT Press, August 2015
 Further readings are provided here: http://ontology.buffalo.edu/smith/
-'''Requirements''': This 2 credit course is open to UB students who complete this [http://ncorwiki.buffalo.edu/index.php/Philosophy_and_Artificial_Intelligence_(Crash_Course) 1 credit course on Philosophy and Artificial Intelligence]. It is also open to any non-UB persons with an undergraduate degree and some relevant experience (for example data science or information engineering). No prior knowledge of ontology is required.
+'''Requirements''':
+*This course is open to all persons with an undergraduate degree and some relevant experience (for example in philosophy, data science or information engineering).
+*No prior knowledge of ontology is required.
+In order to receive a grade and course credit students will be required to have reviewed in a timely manner all provided videos and any accompanying recommended reading and provided questions in response. Grading will be on the basis of contributed questions, contributions to the on-line class discussions prompted by these questions, and quality of any written work, powerpoint, youtube or Protege material.
+Each 3 credit hour student will be required to create one such video for presentation in the final class session. Examples of student videos created in comparable classes in the past are available [http://ncorwiki.buffalo.edu/index.php/Analytic_Metaphysics#April_26:_Presentations_of_Student_Projects_1 here] and [http://ncorwiki.buffalo.edu/index.php/Ontological_Engineering_2014#November_24:_Presentations_of_Student_Projects_1 here].
+*Your video should be 20 minutes long; it will be graded on the basis of clarity and force of argument, interestingness of content, and quality of delivery, including response to questions.
+*The video should be based on a powerpoint presentation of approximately 20 slides. The slides should provide a minimal amount of text (using 24 point font or above), together with accompanying graphics, for example charts representing data. You should not ''read'' the slides -- rather, you should use the slides as summaries of the successive points you want to make, and present these points ''ex tempore''.
+All class participants should communicate by email with Dr Smith to determine topic of your written essay.
-In order to receive a grade and course credit students will be required to have reviewed in a timely manner all provided videos and any accompanying recommended reading. Grading will be on the basis of contributions to the on-line class discussion forum and on the quality and content of a 20 minute youtube video (with accompanying essay and powerpoint slide deck) on some topic in the field of applied ontology. Each student will be required to create one such video for presentation in the final class session on May 8. Examples of student videos created in comparable classes in the past are available [http://ncorwiki.buffalo.edu/index.php/Analytic_Metaphysics#April_26:_Presentations_of_Student_Projects_1 here] and [http://ncorwiki.buffalo.edu/index.php/Ontological_Engineering_2014#November_24:_Presentations_of_Student_Projects_1 here].
+'''Grading''' will be determined as follows:
-*Your video should be 20 minutes long; it will be graded on the basis of clarity and force of argument, interestingness of content, and quality of delivery.
-*The video should be based on a powerpoint presentation of approximately 20 slides. The slides should provide a minimal amount of text (using 30 point font or above), together with accompanying graphics, for example charts representing data. You should not ''read'' the slides -- rather, you should use the slides as summaries of the successive points you want to make, and present these points ''ex tempore''.
-*The video should be accompanied by an essay presenting the points you make and providing literature references, the whole amounting to at least 3000 words. A short draft of your essay should be submitted to Dr Smith by March 31 at the latest.
-Class participants should communicate by email with Dr Smith to determine topic and scope of your video presentation and accompanying materials.
-'''Grading''' will be based on:
+-credit hour students:
+:1. submitted questions (35%)
+:2. contributions to email discussions (5%)
+:3. essay (30%)
+:4. participation in face-face sessions after May 10 (30%)
-:1. forum participation (25%)
+-credit hour students
-:2. 20 minute youtube video (25%)
+:1. submitted questions (15%)
-:3. associated powerpoint slides (25%)
+:2. contributions to email discussions (5%)
-:4. associated essay (25%)
+:3. participation in face-face sessions after May 10 (20%)
+:4. essay (30%)
+:5. powerpoint (10%)
+:6. presentation (20%)
+:7. essay on the topic of their video presentation; length (for graduate students): ca. 3000 words; (for undergraduate students): ca. 1500 words
 For policy regarding incompletes see [http://grad.buffalo.edu/Academics/Policies-Procedures/Grading-Procedures.html here]
 For academic integrity policy see [http://www.grad.buffalo.edu/policies/academicintegrity.php here]

Applied Ontology, Spring 2022: Difference between revisions

Latest revision as of 18:17, 10 May 2022

January 31: Introduction to Ontology

February 7: Introduction to Applied Ontology

February 14: Ontology and Artificial Intelligence

Feb 21: Towards a Standard Upper Level Ontology

Feb 24: Face-to-Face Question-and-Answer Session

Feb 28: Basic Formal Ontology

Mar 7: Drill

Mar 10: Face-to-Face Question-and-Answer Session

Mar 14: Ontology of Philosophy

Mar 28 Applied Ontology in Geospatial Science

April 4: Ontology of Military Domains

Apr 11: Ontology and Intelligence Analysis

Apr 14: Face-to-Face Q&A Meeting

Apr 18: Ontology of Space

Apr 25: Ontology of Biomedicine

May 2: Artificial Intelligence

May 5: Q&A Session

May 12: 9:00-10:30am: Student video presentations

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