Information Science for Bioinformatics
GNET 211, Spring 2006, section 001
Tuesday and Thursday, 9:00am - 10:45am 214 Manning Hall
Feb 14th - Mar 21st
School of Information and Library Science

Course Outline and Objectives
Class Policies and Grading
Schedule 
Resources

Course Outline and Objectives

Outline (by class)

1. Introduction, Database Concepts and Architecture, ER Modeling
2. Relational Model and Related Topics
3. SQL
4. Build and Test a Database Lab
5. Classification, Indexing, Searching
6. Information Retrieval, Digital Libraries, Standards
7. Information Retrieval Lab and Practice
8. Metadata, Ontologies

Objectives

1. Develop a general understanding of databases, and specific understanding of the relational database model.
2. Gain experience with both the theoretical and practical aspects of database design.
3. Understand at a high level the major concepts of information science, including classification, indexing, retrieval, and searching.
4. Practice and become facile with searching bioinformatics and biomedical databases.
5. Understand why metadata and ontology standards are important, and the relevance of digital libraries.

Class Policies and Grading

Class Policies

1. I will always be prepared for class and will start class on time. If unforeseeable circumstances prevent this for any reason, I will try to notify you beforehand if at all possible. I expect the same of my students: be prepared for class, be ready to start class on time, and try to let me know by email if you can't be there.

2. Class notes and most materials, as well as the class syllabus, policies, and schedule are available online from this web page. The class notes are available so that you don't have to write down the basic information presented during class, hopefully allowing you to concentrate on the discussions and additional information presented in class.

3. Labs and assignments should be turned in at the start of the class on which they are due. Databases (in Access) should be emailed to me. All other work (descriptions, ER diagrams, etc) should be printed out and handed in at the start of class. All ER diagrams should fit on a single page. Your access file should be named like jones-A3.mdb, for Assignment 3. Similarily, on your printed work, each page must include your name, and the assignment. Please make sure everything is correct before turning in, so that I receive one and only one correct version of the your homework.

4. Late assignments. Any assignment received after the start of class when it is due, will be considered late. Late assignments can still be turned in for credit. They are penalized by the following formula: they are docked 5 points for each day they are late (not counting weekends). Each assignment is graded on a 100 point scale. Thus, an assignment due Tuesday at 11:00am and turned anytime between Wed at 11:01am and Thursday at 11:00am would be graded on the usual 100 point scale, and then have 10 points (two days late) deducted from the total.

5. You are expected and encouraged to participate in discussions and exercises in class. I will ask students to explain portions of what was to be read in preparation for a class, as well as to come to the board to work exercises. Part of your grade will be determined by the quality of your participation and your willingness to participate.

6. Please be sure to subscribe to the class listserv. Click here to join the GNET 211 Class Listserv. On the form just fill in your email address; leave the other fields set to their defaults, then click Save to add yourself to the list. To send a message to the listserv, you send it to "gnet211@listserv.unc.edu", and it will be distributed to everyone in the class. Sign up on the listserv immediately after the first class! (We may not use this if very small class--check with me at first class)

7. Reading assignments should be done before the class for which they are assigned so you can ask questions and participate in discussions. The textbook is not light reading. You may find it easier to skim the reading before class and then read it again in more detail after we have discussed it. If you do this, do not skip the second reading.

8. If there is something you don't understand, please ask about it! If you don't want to ask during class, you may ask me during office hours, come see me at some other time, post your question to the listserv, or ask me over email. Your classmates may well be your best resource for Access 2000 questions.

9. All assignments and labs are to be completed individually. You are, however, encouraged to talk to one another about issues of a general nature (for example, for questions like "How do I do <fill in the blank> in Access or MySQL?"). 

10. Honor Code: The principles of academic honesty, integrity, and responsible citizenship govern the performance of all academic work and student conduct at the University as they have during the long life of this institution. Your acceptance of enrollment in the University presupposes a commitment to the principles embodied in the Code of Student Conduct and a respect for this most significant Carolina tradition. Your reward is in the practice of these principles. Your participation in this course comes with the expectation that your work will be completed in full observance of the Honor Code. Academic dishonesty in any form is unacceptable, because any breach in academic integrity, however small, strikes destructively at the University's life and work. (From the 8/1/1992 letter to the faculty, signed by Paul Hardin, Chancellor, and John Moody, Student Body President.)

11. SILS Resources: You may be using SILS library and lab material during the course of the semester. Please remember that many of your fellow students also need to use the same material. Follow the proper checkout procedures and return materials promptly to be a good SILS citizen. (SILS Information Resources Committee). Note that the SILS library staff and myself have made an effort to make all the classmaterials available electronically (either the original online or a digitized copy). Please use those if possible instead of the printed copy.

Grading

    A1    15%
    A2    15%
    A3    15%
    A4    15%

All assignments and your final grade will be graded on the following scale:

Resources

Company database as shown in Access 2000 relationship window. This is a screenshot of what the Company database example from the textbook would look like in the Access 2000 relationship window. Note especially how the recursive relationship (supervises) with Employee as handled -- you have to make a copy of the Employee table in the relationship window (shown as Employee_1) in order to draw the connection between the foreign key SuperSSN and the primary key SSN in the Employee table. Whenever you have a recursive relationship, you will always have to show two copies of the table that represents the recursive entity in your relationship window.

The Company Database is also available as an Access file. This can be helpful for testing queries, etc.

Microsoft Media Order Page at the Ram Shop. Students can purchase Microsoft Office 2000 Professional (which includes Access 2000) for $10.00 from the Ram Shop. 

Access 2000 Workshops Offered by ATN. This page describes the workshops offered by ATN in Access 2000. All of these workshops are free, but they do fill up quickly. I would strongly encourage you to attend one or more of these workshops to learn about how to work with Access. In addition, there is information on this page about Computer-Based Training (CBT) modules for Access. These are probably a little more basic than most of you will want, but they are also free and can be used from any computer on the campus network.

Jose's Database Programming Corner - The Relational Database Model. A nice page if you're looking for supplementary material about the relational model.

DB Checklist. This is a checklist you can use as you are completing your labs to help you determine if you have completed all the steps.

Company ER Diagram. This diagram represents the same situation as Fig. 3.2 (p. 46) in the textbook, but using the notation I will expect you to learn and to use for ER diagrams that you turn in for this course.

Example ER Diagram Notation in FlowCharter. Example Flowcharter file containing simple diagram that contains most of the notation you'll need for this course. You can use this as template to get quick access to the graphical annotations you'll use in your assignments. Note if this doesn't open correctly, please retrieve original file from ILS G:\bmh\read_shared\ExampleDiagram.igx (kiwi).

Steps for Converting an E-R Diagram into a Relational Database Schema. These are the same steps as those given in the text, but without the formal notation and including examples from the Company database.

Notes on B+ Trees. These notes expand a bit on what we cover in class, and provide a couple more examples.

This page was last modified on Oct 30, 2003, by Bradley Hemminger. Address questions and comments about this page to him at bmh@ils.unc.edu
© Bradley M. Hemminger