Applied Ontology: Difference between revisions
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'''Course Structure:''' This will be a three credit hour '''on-line''' graduate seminar. It will be taught on Mondays from January 30 to May 8, 2017 through the medium of a series of 2-hour long videos incorporating presentation of powerpoint slides and question-answer sessions. Links to course videos will be provided each Sunday at 9am. Students will be required to watch the video class some time within 48 hours. In each week (starting on Mondays at 9am) class participants will be able to post questions, discussion comments and responses to the class email forum relating to the video from the relevant week. The final session or sessions (depending on the number of class participants) will consist in youtube videos (ca. 20 minutes in length) created by the students in the class. | '''Course Structure:''' This will be a three credit hour '''on-line''' graduate seminar. It will be taught on Mondays from January 30 to May 8, 2017 through the medium of a series of 2-hour long videos incorporating presentation of powerpoint slides and question-answer sessions. Links to course videos will be provided each Sunday at 9am. Students will be required to watch the video class some time within 48 hours. In each week (starting on Mondays at 9am) class participants will be able to post questions, discussion comments and responses to the class email forum relating to the video from the relevant week. The final session or sessions (depending on the number of class participants) will consist in youtube videos (ca. 20 minutes in length) created by the students in the class. | ||
'''Course Description:''' An ontology is a structured collection of terms used to tag data with the goal of making data deriving from heterogeneous sources | '''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 such as the Gene Ontology allows researchers on aging to use data from cell biologists, yeast biologists, cancer biologists, geneticists, and gerontologists, because all of these data are tagged using common ontologies (which provide a shared vocabulary which both experts and non-experts can use). | ||
Ontology is an important tool of for data search and retrieval, analysis, comparison and integration. It used in a wide variety of domains from biomedicine to cyberwarfare and from finance to industrial engineering. The course will provide an introduction to ontology from an application oriented point of view, focusing on the identification and use of best practices for ontology development, and on the development of plug-and-play ontology modules for re-use in different areas. | Ontology is an important tool of for data search and retrieval, analysis, comparison and integration. It used in a wide variety of domains from biomedicine to cyberwarfare and from finance to industrial engineering. The course will provide an introduction to ontology from an application oriented point of view, focusing on the identification and use of 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. | ||
'''Example Ontologies''': | '''Example Ontologies''': | ||
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::[http://obofoundry.org OBO (Open Biomedical Ontologies) Foundry] | ::[http://obofoundry.org OBO (Open Biomedical Ontologies) Foundry] | ||
::[https://jbiomedsem.biomedcentral.com/articles/10.1186/2041-1480-4-43 The Environment Ontology] | ::[https://jbiomedsem.biomedcentral.com/articles/10.1186/2041-1480-4-43 The Environment Ontology] | ||
::[ | ::[https://www.youtube.com/watch?v=b4kULamlFaM Ontology for General Medical Science] | ||
'''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://mitpress.mit.edu/index.php?q=books/building-ontologies-basic-formal-ontology Building Ontologies with Basic Formal Ontology], Cambridge, MA: MIT Press, August 2015 | ||
Revision as of 15:55, 10 October 2016
Title: PHI 549 Applied Ontology
Faculty: Barry Smith
Registration: Details will be provided in due course. You can find preliminary orientation here under Part Time/Graduate.
Course Structure: This will be a three credit hour on-line graduate seminar. It will be taught on Mondays from January 30 to May 8, 2017 through the medium of a series of 2-hour long videos incorporating presentation of powerpoint slides and question-answer sessions. Links to course videos will be provided each Sunday at 9am. Students will be required to watch the video class some time within 48 hours. In each week (starting on Mondays at 9am) class participants will be able to post questions, discussion comments and responses to the class email forum relating to the video from the relevant week. The final session or sessions (depending on the number of class participants) will consist in youtube videos (ca. 20 minutes in length) created by the students in the class.
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 such as the Gene Ontology allows researchers on aging to use data from cell biologists, yeast biologists, cancer biologists, geneticists, and gerontologists, because all of these data are tagged using common ontologies (which provide a shared vocabulary which both experts and non-experts can use). Ontology is an important tool of for data search and retrieval, analysis, comparison and integration. It used in a wide variety of domains from biomedicine to cyberwarfare and from finance to industrial engineering. The course will provide an introduction to ontology from an application oriented point of view, focusing on the identification and use of 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.
Example Ontologies:
Text: Robert Arp, Barry Smith and Andrew Spear, Building Ontologies with Basic Formal Ontology, Cambridge, MA: MIT Press, August 2015
Further readings are provided here: http://ontology.buffalo.edu/smith/
Example videos are provided here: https://www.youtube.com/user/hxo3nql/playlists
Requirements: This course is open to all persons with an undergraduate degree and some relevant experience (for example in data scientists, information engineers, terminology researchers). 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. 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 here and here.
Grading will be based on:
- 1. forum participation (25%)
- 2. 20 minute youtube video (25%)
- 3. associated powerpoint slides (25%)
- 4. associated essay (25%)
For policy regarding incompletes see here
For academic integrity policy see here
