605.624.81 - Logic: Systems, Semantics, and Models

Computer Science
Spring 2024


Traditionally, logic is the study of correct reasoning. In the last few decades, logic has become increasingly important to knowledge representation -- a subfield of artificial intelligence concerned with developing representations of the world (often called ontologies) that aid computers in understanding and making sense of data. This course will promote both a theoretical and practical understanding of logic as a stepping stone for working in contemporary knowledge representation. We will begin with a review of categorical, propositional, and predicate logic. We will then survey modal logics, which include systems that represent necessity and probability, as well as other systems that represent time, and moral notions such as obligation and permissibility. The second half of the course will then introduce the semantic web and ontology engineering. Students will explore the top-level ontology Basic Formal Ontology (BFO) and gain familiarity using mereological and temporal relations. In addition, students will create ontologies in the web ontology language (OWL2) and use the language SPARQL to query knowledge graphs. Students will have the option of writing either a research paper or creating an ontology in OWL with slides as part of a final project.


Profile photo of J. Neil Otte.

J. Neil Otte

Course Structure

The course materials are divided into modules which can be accessed by clicking Modules on the course menu. A module will have several sections including the overview, content, readings, discussions, and assignments. You are encouraged to preview all sections of the module before starting. Most modules run for a period of seven (7) days, exceptions are noted in the Course Outline. You should regularly check the Calendar and Announcements for assignment due dates.

Course Topics

Course Topics

Course Goals

Specific Outcomes for this course include:



Required Software

Protege Ontology Editor


Student Coursework Requirements

Course Expectations & Grading

Every class will generally consist of a set of video lectures, wiki discussions, and assignments. These assignments will vary in form, from translating English sentences into logical expressions, creating truth tables, executing deductive proofs, and truth trees, to writing short response papers and implementing ontologies.


Inference Rules

In the course, we introduce a system of natural deduction and a set of inference rules. Students are encouraged to finish all assignments using only these rules. However, students who wish to introduce their own rules in order to shorten proofs may do so, provided they first prove the validity of such rules in a separate proof using no rules other than those we have introduced in the course. No exceptions allowed.


Final Project

Students must choose at the end of the course whether to write a paper targeted for an academic journal on a topic relevant to the course, or to create an ontology using the ontology editor Protégé, along with a set of slides describing it.


Final Paper Option


The paper should be 8-12 pages in Times New Roman, double spaced, with a references section following MLA, and must not have a cover page. Topics for final papers should be approved with the instructor in advance (the purpose of which is to ensure the topic is germane to the class, and brainstorm research tips). Sample paper topics may include:


Final Ontology Option


Students who choose to create an ontology are advised to start early, as these topics are only covered in the latter half of the course. The ontology should be implemented in the format Turtle, should be able to be opened in Protégé, and should seek to represent some domain of interest. Every class and relation must be well-defined and import at least one ontology (e.g. Basic Formal Ontology) that it uses and extends. The classes must be relevant to the domain, or be required for returning a particular query of interest. In addition, the ontology must be accompanied by a slide deck of PowerPoint slides that present the ontology. The ‘notes’ section of each slide should be filled out, discussing the content of each slide as though you these were a transcript of a presentation on the ontology. This presentation should include describing the domain of the ontology, describing how the ontology represents that domain, and describing how the ontology might be used to solve a problem within that domain.


Examples include:

This course will consist of the following basic student requirements:

Preparation and Participation (30% of Final Grade Calculation)

You are responsible for carefully reading all assigned material and being prepared for discussion.

Post your initial response to the discussion questions by the evening of day 3 for that module week. Posting a response to the discussion question is part one of your grade for module discussions (i.e., Timeliness).

Part two of your grade for module discussions is your interaction (i.e., responding to classmate postings with thoughtful responses) with at least two classmates (i.e., Critical Thinking). Just posting your response to a discussion question is not sufficient; I want you to interact with your classmates: debate, engage, brainstorm, and share. Be detailed in your postings and in your responses to your classmates' postings. Feel free to agree or disagree with your classmates, but (of course) always ensure that your postings are civil and constructive.

I will monitor module discussions and will respond to some of the discussions as they are posted.

Evaluation of preparation and participation is based on contribution to discussions.

Preparation and participation is evaluated by the following grading elements:

Preparation and participation is graded as follows:

Assignments (40% of Final Grade Calculation) and Final Project (30% of Final Grade Calculation)

Written assignments should be turned in as .docx files. These will be graded using Word’s trach change feature. Tree proofs, Venn diagrams, and formal proofs may be graphically drawn or hand drawn, scanned, and then submitted. They must be submitted as PDF files. Any scanned assignment should be examined carefully to ensure that it is clearly legible (illegible scans will result in a deduction of points).

All assignments are due according to the dates in the Calendar.

Late submissions will be reduced by one letter grade for each week late (no exceptions without prior coordination with the instructors).

If, after submitting a written assignment you are not satisfied with the grade received, you are encouraged to redo the assignment and resubmit it. If the resubmission results in a better grade, that grade will be substituted for the previous grade.

Important: Formal proofs will receive partial credit even if they are not finished, or where they contain mistakes. This should provide ample reason for showing your work and getting as far as you can, even if you find yourself unable to finish.

Written assignments and final projects are graded as follows:

For those who choose creating an ontology as the final option, the ontology and the PowerPoint slides shall be graded as follows:

Grading Policy

Assignments are due according to the dates posted in your Canvas course site. You may check these due dates in the Course Calendar or the Assignments in the corresponding modules. I will post grades one week after assignment due dates.

A grade of A indicates achievement of consistent excellence and distinction throughout the course—that is, conspicuous excellence in all aspects of assignments and discussion in every week.

A grade of B indicates work that meets all course requirements on a level appropriate for graduate academic work. These criteria apply to both undergraduates and graduate students taking the course.

EP uses a +/- grading system (see “Grading System”, Graduate Programs catalog, p. 10).

100-98 = A+ 97-94 = A 93-90 = A− 89-87 = B+ 86-83 = B 82-80 = B− 79-77 = C+ 76-73 = C 72-70 = C− 69-67 = D+ 66-63 = D <63 = F

Course Policies

Academic Integrity

Academic Misconduct Policy

All students are required to read, know, and comply with the Johns Hopkins University Krieger School of Arts and Sciences (KSAS) / Whiting School of Engineering (WSE) Procedures for Handling Allegations of Misconduct by Full-Time and Part-Time Graduate Students.

This policy prohibits academic misconduct, including but not limited to the following: cheating or facilitating cheating; plagiarism; reuse of assignments; unauthorized collaboration; alteration of graded assignments; and unfair competition. You may request a paper copy of this policy at this by contacting jhep@jhu.edu.


The strength of the university depends on academic and personal integrity. In this course, you must be honest and truthful, abiding by the Computer Science Academic Integrity Policy:

Cheating is wrong. Cheating hurts our community by undermining academic integrity, creating mistrust, and fostering unfair competition. The university will punish cheaters with failure on an assignment, failure in a course, permanent transcript notation, suspension, and/or expulsion. Offenses may be reported to medical, law or other professional or graduate schools when a cheater applies.

Violations can include cheating on exams, plagiarism, reuse of assignments without permission, improper use of the Internet and electronic devices, unauthorized collaboration, alteration of graded assignments, forgery and falsification, lying, facilitating academic dishonesty, and unfair competition. Ignorance of these rules is not an excuse.

Academic honesty is required in all work you submit to be graded. Except where the instructor specifies group work, you must solve all homework and programming assignments without the help of others. For example, you must not look at anyone else’s solutions (including program code) to your homework problems. However, you may discuss assignment specifications (not solutions) with others to be sure you understand what is required by the assignment.

If your instructor permits using fragments of source code from outside sources, such as your textbook or on-line resources, you must properly cite the source. Not citing it constitutes plagiarism. Similarly, your group projects must list everyone who participated.

Falsifying program output or results is prohibited.

Your instructor is free to override parts of this policy for particular assignments. To protect yourself: (1) Ask the instructor if you are not sure what is permissible. (2) Seek help from the instructor, TA or CAs, as you are always encouraged to do, rather than from other students. (3) Cite any questionable sources of help you may have received.

On every exam, you will sign the following pledge: "I agree to complete this exam without unauthorized assistance from any person, materials or device. [Signed and dated]". Your course instructors will let you know where to find copies of old exams, if they are available.

You can find more information about university misconduct policies on the web at these sites:

Policy on Disability Services

Johns Hopkins University (JHU) is committed to creating a welcoming and inclusive environment for students, faculty, staff and visitors with disabilities. The University does not discriminate on the basis of race, color, sex, religion, sexual orientation, national or ethnic origin, age, disability or veteran status in any student program or activity, or with regard to admission or employment. JHU works to ensure that students, employees and visitors with disabilities have equal access to university programs, facilities, technology and websites.

Under Section 504 of the Rehabilitation Act of 1973, the Americans with Disabilities Act (ADA) of 1990 and the ADA Amendments Act of 2008, a person is considered to have a disability if c (1) he or she has a physical or mental impairment that substantially limits one or more major life activities (such as hearing, seeing, speaking, breathing, performing manual tasks, walking, caring for oneself, learning, or concentrating); (2) has a record of having such an impairment; or (3) is regarded as having such an impairment class. The University provides reasonable and appropriate accommodations to students and employees with disabilities. In most cases, JHU will require documentation of the disability and the need for the specific requested accommodation.

The Disability Services program within the Office of Institutional Equity oversees the coordination of reasonable accommodations for students and employees with disabilities, and serves as the central point of contact for information on physical and programmatic access at the University. More information on this policy may be found at the Disabilities Services website or by contacting (410) 516-8075.

Disability Services

Johns Hopkins Engineering for Professionals is committed to providing reasonable and appropriate accommodations to students with disabilities.

Students requiring accommodations are encouraged to contact Disability Services at least four weeks before the start of the academic term or as soon as possible. Although requests can be made at any time, students should understand that there may be a delay of up to two weeks for implementation depending on the nature of the accommodations requested.

Requesting Accommodation

New students must submit a Disability Services Graduate Registration Form  along with supporting documentation from a qualified diagnostician that:

Questions about disability resources and requests for accommodation at Johns Hopkins Engineering for Professionals should be directed to:

EP Disability Services Phone: 410-516-2306 Fax: 410-579-8049 E-mail: ep-disability-svcs@jhu.edu

Academic Policies

Deadlines for Adding, Dropping and Withdrawing from Courses

Students may add a course up to one week after the start of the term for that particular course. Students may drop courses according to the drop deadlines outlined in the EP academic calendar (https://ep.jhu.edu/student-services/academic-calendar/). Between the 6th week of the class and prior to the final withdrawal deadline, a student may withdraw from a course with a W on their academic record. A record of the course will remain on the academic record with a W appearing in the grade column to indicate that the student registered and withdrew from the course.

Academic Misconduct Policy

All students are required to read, know, and comply with the Johns Hopkins University Krieger School of Arts and Sciences (KSAS) / Whiting School of Engineering (WSE) Procedures for Handling Allegations of Misconduct by Full-Time and Part-Time Graduate Students.

This policy prohibits academic misconduct, including but not limited to the following: cheating or facilitating cheating; plagiarism; reuse of assignments; unauthorized collaboration; alteration of graded assignments; and unfair competition. Course materials (old assignments, texts, or examinations, etc.) should not be shared unless authorized by the course instructor. Any questions related to this policy should be directed to EP’s academic integrity officer at ep-academic-integrity@jhu.edu.

Students with Disabilities - Accommodations and Accessibility

Johns Hopkins University values diversity and inclusion. We are committed to providing welcoming, equitable, and accessible educational experiences for all students. Students with disabilities (including those with psychological conditions, medical conditions and temporary disabilities) can request accommodations for this course by providing an Accommodation Letter issued by Student Disability Services (SDS). Please request accommodations for this course as early as possible to provide time for effective communication and arrangements.

For further information or to start the process of requesting accommodations, please contact Student Disability Services at Engineering for Professionals, ep-disability-svcs@jhu.edu.

Student Conduct Code

The fundamental purpose of the JHU regulation of student conduct is to promote and to protect the health, safety, welfare, property, and rights of all members of the University community as well as to promote the orderly operation of the University and to safeguard its property and facilities. As members of the University community, students accept certain responsibilities which support the educational mission and create an environment in which all students are afforded the same opportunity to succeed academically. 

For a full description of the code please visit the following website: https://studentaffairs.jhu.edu/policies-guidelines/student-code/

Classroom Climate

JHU is committed to creating a classroom environment that values the diversity of experiences and perspectives that all students bring. Everyone has the right to be treated with dignity and respect. Fostering an inclusive climate is important. Research and experience show that students who interact with peers who are different from themselves learn new things and experience tangible educational outcomes. At no time in this learning process should someone be singled out or treated unequally on the basis of any seen or unseen part of their identity. 
If you have concerns in this course about harassment, discrimination, or any unequal treatment, or if you seek accommodations or resources, please reach out to the course instructor directly. Reporting will never impact your course grade. You may also share concerns with your program chair, the Assistant Dean for Diversity and Inclusion, or the Office of Institutional Equity. In handling reports, people will protect your privacy as much as possible, but faculty and staff are required to officially report information for some cases (e.g. sexual harassment).

Course Auditing

When a student enrolls in an EP course with “audit” status, the student must reach an understanding with the instructor as to what is required to earn the “audit.” If the student does not meet those expectations, the instructor must notify the EP Registration Team [EP-Registration@exchange.johnshopkins.edu] in order for the student to be retroactively dropped or withdrawn from the course (depending on when the "audit" was requested and in accordance with EP registration deadlines). All lecture content will remain accessible to auditing students, but access to all other course material is left to the discretion of the instructor.