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OHSU Online · School of Medicine

Information Retrieval
BMI-514

  • Spring 2019
  • 3 Credits
  • 04/01/2019 to 06/21/2019
  • Modified 02/25/2019

Description

This course is designed to provide the student with an understanding of the theory, implementation, and evaluation methods of text-based information retrieval systems. It covers health and biomedical information, current indexing and retrieval practice, system evaluation, research efforts investigating new approaches to indexing and retrieval, and digital libraries.

Prerequisite: BMI 510/610.

Offering: On Campus: Spring; Online: Spring

Contact Information

Meeting Times

All class lectures and homework quizzes are online. The lectures cover the textbook content, with updates since publication of the textbook provided on the textbook Web site (see below). Students have interactive discussion in the Sakai forums

Materials

There are no required readings for the course, and only materials from the lectures will be covered on the homework and final exams. However, the third edition of the instructor’s book, Information Retrieval: A Health and Biomedical Perspective (Spring-Verlag, 2009) follows the course closely and can be used for those desiring a textbook to read. (The book is somewhat dated, and I aim for a new version to be released in 2020.) Please make sure to use the third edition. The book is available from Amazon.com in paper and Kindle forms. Students can also read the chapter updates on the textbook Web site (http://www.irbook.info/updates-toc.html), which may be covered in the lectures.

Course Goals

Course Competencies, Outcomes, and Objectives

Assessment

Assignments

 

There are weekly homework assignments on the Sakai system consisting of multiple-choice homework quizzes. These are due one week after the material is posted.

 

Final Examination

 

There is an open-book final examination, which consists of short answer questions. Any material assigned for reading may appear, with emphasis on material that is covered in class.

 

Course Projects

 

A course project is required of all students, due June 7th at 5 pm Pacific time.  The project may consist of:

  • A 10-15 page paper on a particular line of work on some aspect of indexing, retrieval, or evaluation
  • A 10-15 page detailed proposal for a new approach to indexing, retrieval, or evaluation
  • Implementation of a computer program implementing some aspect of indexing, retrieval, or evaluation, with 10-15 pages of commented code

 

If you choose to write a term paper, you should explore a topic of interest beyond what we cover in class. You should pick a topic that interests you, search for information about it in reputable sources, and write it up in a coherent and readable manner. You must not simply re-hash material we cover in class.

One of the big challenges students face with this assignment is an appropriate level of focus. You may need to do some searching to determine what that level of focus is. You want a topic that you can reasonably describe, not necessarily in exhaustive detail, in 10-15 pages. If you have questions about appropriate level of focus, or any other questions, do not hesitate to email the instructor. He and you can even talk by phone if necessary.

Some logistical details about the paper:

  • It should be 10-15 pages double-spaced, including tables, figures, and references, with one-inch margins.
  • It should be a readable narrative and not a series of lists or bulleted items.
  • The text should be your own words and not copied and pasted from other writings. (An on-line plagiarism-checking tool is used.)
  • It should be typed into a Microsoft Word document.
  • The file name should begin with your last name, e.g., Hersh-BMI514.docx, and be uploaded to the Submission site on Sakai (do not email it).
  • The references can be in any format you choose (e.g., APA, Vancouver) as long as they are consistent and have enough information for them to be located (which the instructor occasionally does, since you may pique his interest!).

Grading

 

Grading consists of 30% assignments, 30% final examination, 30% course project, and 10% class participation.

 

The course is graded on a curve, but usually adheres to the following distribution:

A             90-100

A-           85-89

B+          80-84

B             75-79

B-           70-74

C+           65-69

C             60-64

D/F        <60

Course & Instructor Evaluations

Schedule

Date Posted

Topic

Textbook Reading

4/3

Terms, Models, Resources, and Evaluation

1

4/10

Health and Biomedical Information

2

4/17

Content

3

4/24

Indexing

4

5/1

Retrieval

5

5/8

Digital Libraries

6

5/15

Evaluation

7

5/22

System and User Research

8

5/29

Related Topics

9

6/5

Term project due; final exam distributed

 

TBD

Final exam due

 

 

Course Policies and Resources

When Problems Arise

 

It is critical to contact the appropriate person when problems arise:

  • For basic Sakai problems and course issues (e.g., cannot log in, after-hours technical assistance, Course Materials or Forum not available/accessible during regular business hours/days), contact the Sakai Help Desk: Toll-Free - (877) 972-5249; email - [email protected]. Sakai help is available M-F from 8am to 9 pm and weekends from Noon to 5pm.
  • For questions about course content (e.g., do not understand a topic or disagree with homework quiz answer), contact the Teaching Assistant, who will be announced at the beginning of the course:  go to the Email Tab after logging into the course and choose “Associate” role to send message to the TA or post a question in the Forums.

 

When appropriate, all issues will be elevated to Dr. Hersh. While Dr. Hersh does not maintain scheduled office hours, he is readily accessible via email and will respond within 24-48 hours. Appointments to discuss course matters by phone or in person can be arranged via email.

Course Access

 

Every reasonable effort has been made to protect the copyright requirements of materials used in this course.  Class participants are warned not to copy, audio, or videotape in violation of copyright laws.  Journal articles will be kept on reserve at the library or online for student access. Copyright law does allow for making one personal copy of each article from the original article. This limit also applies to electronic sources.

 

To comply with the fair use fair use doctrine of the US copyright law, Sakai course sites close three weeks after grades are posted with the Registrar. Please be sure to download all course material you wish to keep before this time as you will have no further access to your courses.

 

School Policies and Resources

Graduate Studies Guidelines:

Students are responsible for following all OHSU School of Medicine, Graduate Studies, and program/department guidelines & policies. For more information, please visit here. For program/department guidelines & policies, please inquiry with the program/department director and/or coordinator.

School of Medicine Conduct Policy (housed under the graduate studies guidelines section)

Students are responsible for their own academic work. Students are expected to have read and practice principles of academic honesty, as presented in the Graduate Studies Student Handbook.

The School of Medicine reserves the privilege of retaining only those students who, in the judgement of the faculty, satisfy the requirements of scholarship and clinical performance necessary to maintain the highest standards. The Student Handbook has information about academic standards and probation and dismissal policies.

Grading Criteria, Academic Standards, & Release of Final Grades:

Graduate Studies in the OHSU School of Medicine is committed to providing grades to students in a timely manner. Course instructors will provide students with information in writing at the beginning of each course that describes the grading policies and procedures including but not limited to evaluation criteria, expected time needed to grade individual student examinations and type of feedback they will provide.

All coursework applied towards degree requirements must meet the minimum cumulative grade point average of at least 3.0.

Refer to the School of Medicine Graduate Studies Forms & Policies for withdraw, incomplete, and in-progress grading standards. Final course grades will be posted with the OHSU Registrar the Monday following the last day of the term. On those occasions when a grade has not been submitted by the deadline, the following procedure shall be followed:

  1. The Department*/Program** Coordinator will immediately contact the Instructor requesting the missing grade, with a copy to the Program Director and Registrar.
  2. If the grade is still overdue by the end of next week, the Department*/Program** Coordinator will email the Department Chair directly, with a copy to the Instructor and Program Director requesting resolution of the missing grade.
  3. If, after an additional week the grade is still outstanding, the student or Department*/Program** Coordinator may petition the Office of Graduate Studies for final resolution.

*For courses that are run by a specific department.

**For the conjoined courses (course number is preceded by CON) that are run by Graduate Studies.

Graduate Studies Inclement Weather Procedures

Inclement weather procedures can be found here. In the case of inclement weather, the faculty member will email or place a voice-mail greeting on her/his office telephone number by 6:00am on the day of the clinical or class to give instructions to students about the class schedule.

Graduate Studies Copyright Information

Every reasonable effort has been made to protect the copyright requirements of materials used in this course. Class participants are warned not to copy, audio, or videotape in violation of copyright laws. Journal articles will be kept on reserve at the library or online for student access. Copyright law does allow for making one personal copy of each article from the original article. This limit also applies to electronic sources.

DMICE Communication Policy

  1. If the syllabus directs the student to contact the TA before contacting the instructor, the student should do so. Otherwise, the student should contact the instructor and allow 2 business days (not including weekends) for a response.
  2. If the student does not receive a response from the instructor within 2 business days, s/he should contact the TA (if there is one). When contacting the TA s/he should cc the instructor and Diane Doctor at [email protected].
  3. If a student does not receive a response from the TA within 1 business day (not including weekends), s/he should contact Diane Doctor at [email protected] and cc the instructor and the TA.
  4. If Diane does not reply within 1 business day (not including weekends), the student should contact Andrea Ilg at [email protected].
  5. Students having difficulties with Sakai should contact the Sakai Help Desk at [email protected] or at (877) 972-5249. Sakai help is available M-F from 8am to 10-pm and weekends from Noon to 5pm. Do not contact the instructor.

When Problems Arise

It is critical to contact the appropriate person when problems arise:

  • For basic Sakai problems and course issues (e.g., cannot log in, after-hours technical assistance, Course Materials or Forum not available/accessible during regular business hours/days), contact the Sakai Help Desk: Toll-Free - (877) 972-5249; email - [email protected] Sakai help is available M-F from 8 am to 9 pm and weekends from Noon to 5pm.

  • For questions about course content (e.g., do not understand a topic or disagree with homework quiz answer), contact the Teaching Assistant, who will be announced at the beginning of the course: go to the Email Tab after logging into the course and choose “Associate” role to send message to the TA or post a question in the Forums.

Examination Policy

It is OHSU policy that any exam offered online and worth more than 10% of the final course grade must be virtually proctored. In this course, we will be using the services of Examity, a remote proctoring services company. You will be required to schedule your exam three (3) weeks ahead of time. There is no cost to the student. More information will be provided to you regarding setup, scheduling, and requirements in the Course Materials.

Policy number: 02-70-050

Turn It In

In an effort to uphold the principles and practice of academic honesty, faculty members at OHSU may use originality checking systems such as Turnitin to compare a student’s submitted work against multiple sources. To protect student privacy in this process, it will be necessary to remove all personal information, i.e. student name, email address, student u-number, or any other personal information, from documents BEFORE submission.

Sakai and TLC Help Desk

You will learn through the Sakai learning management software at http://sakai.ohsu.edu. The online component includes reading material, lectures (including streaming presentations and handouts), project material, learning assignments, and online discussions.  If you have any technical questions or if you need help logging in, please contact the Sakai Help Desk, which is open Mon – Fri, 8 am – 9 pm and weekends 12 pm – 5 pm, Pacific Time.


Contact Information:

(Toll-free) 877-972-5249

(Web) http://atech.ohsu.edu/help

(Email) [email protected]

Online Etiquette

Please use professional etiquette when communicating with peers and the instructor. This means avoiding aggressive or offensive language, showing respect for others’ opinions and positions, and conducting yourself as if you were face to face with them. Please pay special attention to etiquette in class forums and when using email. If you notice someone violating this policy, please make the instructor and TA aware of the problem.

School Competencies

OHSU Competencies

OHSU Graduation Core Competencies

1.  Professional Knowledge and Skills

Demonstrate competence in the core knowledge, skills, and practices as defined by degree programs and relevant professional licensing and credentialing boards.

2.  Reasoning and Judgement

Demonstrate the ability to identify and define problems, critically compare options, make timely decisions or recommendations, identify uncertainties, and use findings to improve outcomes in light of evolving evidence.

3.  Evidence-Based Practice and Research

Demonstrate the ability to access, evaluate, and apply relevant science knowledge to support evidence-based health care, disease prevention, health promotion and discovery.

4.  Lifelong Learning

Demonstrate the ability to recognize gaps in knowledge and experience through informed self-assessment and reflective practices, and take actions to address those gaps.

5.  Communication

Demonstrate active listening and oral and written communication skills with diverse individuals, communities, and colleagues to ensure effective, culturally appropriate exchange of information.

6.  Professionalism and Ethics

Demonstrate integrity, honesty, knowledge of ethical principles and the standards of professional conduct, and the ability to apply ethical principles in clinical care, research, education or community service.

7.  Teamwork

Demonstrate the abilities required to foster and work effectively within collaborative, team-based environments.

8.  Safety and Quality Improvement

Demonstrate the ability to identify situations that compromise safety and participate in risk reduction and continuous quality improvement.

9.  Systems

Demonstrate an appropriate understanding of evolving health care systems, health and science policy, and resource allocation in order to optimize human health and scientific discovery.

10. Patient/Client-Centered Care

Additionally, clinical degree program graduates will be able to...

Demonstrate the ability to collaborate with diverse individuals, families, and communities to provide quality care that is respectful of and responsive to their preferences, needs, attitudes, beliefs and values.

Institutional Policies and Resources

Statement Regarding Students with Disabilities:

OHSU is committed to inclusive and accessible learning environments in compliance with federal and state law. If you have a disability or think you may have a disability (mental health, attention-related, learning, vision, hearing, physical or health impacts) contact the Office for Student Access at (503) 494-0082 or OHSU Student Access to have a confidential conversation about academic accommodations. Information is also available at Student Access Website. Because accommodations may take time to implement and cannot be applied retroactively, it is important to have this discussion as soon as possible.

Portland State students also have similar resources available via the PSU Disability Resource Center (website http://www.pdx.edu/drc ). Please contact the DRC at tel. (503) 725-4150 or email at [email protected]

Student Evaluation of Courses:

Course evaluation results are extremely important and used to help improve courses and the learning experience of future students. Responses will always remain anonymous and will only be available to instructors after grades have been posted. The results of scaled questions and comments go to both the instructor and their unit head/supervisor. Refer to Student Evaluation of Courses and Instructional Effectiveness, *Policy No. 02-50-035.

*To access the OHSU Student Evaluation of Courses and Instructional Effectiveness Policy, you must log into the OHSU O2 website.

Copyright Information:

Copyright laws and fair use policies protect the rights of those who have produced the material. The copy in this course has been provided for private study, scholarship, or research. Other uses may require permission from the copyright holder. The user of this work is responsible for adhering to copyright law of the U.S. (Title 17, U.S. Code). To help you familiarize yourself with copyright and fair use policies, the University encourages you to visit its Copyright Web Page

Sakai course web sites contain material protected by copyrights held by the instructor, other individuals or institutions. Such material is used for educational purposes in accord with copyright law and/or with permission given by the owners of the original material. You may download one copy of the materials on any single computer for non-commercial, personal, or educational purposes only, provided that you (1) do not modify it, (2) use it only for the duration of this course, and (3) include both this notice and any copyright notice originally included with the material. Beyond this use, no material from the course web site may be copied, reproduced, re-published, uploaded, posted, transmitted, or distributed in any way without the permission of the original copyright holder. The instructor assumes no responsibility for individuals who improperly use copyrighted material placed on the web site.

Syllabi Changes and Retention:

Syllabi are considered to be a learning agreement between students and the faculty of record. Information contained in syllabi, other than the minimum requirements, may be subject to change as deemed appropriate by the faculty of record in concurrence with the academic program and the Office of the Provost. Refer to the *Course Syllabi Policy, 02-50-050.

*To access the OHSU Course Syllabus Policy, you must log into the OHSU O2 website.

Commitment to Diversity & Inclusion:

OHSU is committed to creating and fostering a learning and working environment based on open communication and mutual respect. If you encounter sexual harassment, sexual misconduct, sexual assault, or discrimination based on race, color, religion, age, national origin, veteran’s status, ancestry, sex, marital status, pregnancy or parenting status, sexual orientation, gender identity, disability or any other protected status please contact the Affirmative Action and Equal Opportunity Department at 503-494-5148 or [email protected]. Inquiries about Title IX compliance or sex/gender discrimination and harassment may be directed to the OHSU Title IX Coordinator at 503-494-0258 or [email protected]

Modified Operations, Policy 01-40-010:

Students should review the Student Portal, O2, or call OHSU’s weather alert line at 503-494-9021 for the most up-to-date information on OHSU-wide modified operations which include but are not limited to delays or closures for inclement weather. For specific campus information, outside of Portland, check the following sites:

OHSU Resources Available to Students*:

Registrar’s Office
Mackenzie Hall, Rm. 1120
503-494-7800; Email the Registrar

Student Registration Information:
To Register for Classes

OHSU ITG Help Desk
Regular staff hours are 6 a.m. to 6 p.m., Monday through Friday, but phones are answered seven days a week, 24 hours a day. Call 503 494-2222.

Teaching and Learning Center
Academic Support Counseling and Sakai Course Management System, please contact the TLC Help Desk at 877-972-5249 or email TLC Help Desk

Concourse Syllabus Management
For help with accessing your Concourse Syllabus:  Please contact the Sakai help Desk for all other Concourse inquiries please visit the Concourse Tutorial Website or please contact the Mark Rivera at [email protected] or call 503-494-0934

Public Safety

OHSU Public Safety

SOU - Ashland Campus Public Safety

  • For Emergencies dial 911
  • Officer Assistance: (541) 552-6911

WOU - Monmouth Campus Public Safety

  • Emergency: 503-838-9000
  • Main Office (Open 24/7): 503-838-8481

EOU - La Grande Campus Public Safety

  • Emergency: 911
  • Camus Security Non Emergency: 541-962-3911

OIT - Klamath Falls Campus Public Safety

  • Emergency: 911 or 541-885-0911
  • Camus Security Non Emergency: 541-885-1111

*Joseph B. Trainer Health & Wellness Center
Baird Hall, Rm. 18 (Primary Care) and Rm. 6 (Behavioral Health)
503-494-8665; For urgent care after hours, 503-494-8311 and ask for the Nurse on call.
Wellness Center Information  
Wellness Center Website

*Exceptions include Public Health students who have selected PSU as their primary providers and students whose home campus is a satellite campus or online. If your home institution is not on the Portland campus, contact your home institution student support services for more information.

Ombudsman Office
Gaines Hall, Rm. 117
707 SW Gaines Street, Portland, OR 97239
503-494-5397; Contact Ombudsman; Ombudsman Website

Library: Biomedical Information Communication Center
BICC Library Hours of Operation

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