Conceptual data modeling for bioinformatics.

Erich Bornberg-Bauer and Norman W. Paton. (2002). Briefings in Bioinoformatics. Vol. 3. No. 2. 166-180.

Mai NguyenBUS 550, Spring 2013

Dr. Minder Chen

Bioinformatics

…the field of science in which biology, computer science, and information technology merge to form a single discipline.

Biology (Source)

DataInformation

Processing and System

Human Genome Project

identify all the approximately 20,000-25,000 genes in human DNA,

determine the sequences of the 3 billion chemical base pairs that make up human DNA

store this information in databases,

improve tools for data analysis,

transfer related technologies to the private sector, and

address the ethical, legal, and social issues (ELSI) that may arise from the project.

Data Data Data Data,…..

Databases

http://www.taverna.org.uk/introduction/taverna-in-use/bioinformatics/

Conceptual Data Modeling (CDM)

Make explicit the structural properties of data, and as such are useful for capturing, refining, and communicating details about the data in a laboratory or database.

Entity 1

*A type of notation that describes entity types and relationships.

Entity 2

Attributes/

properties

The design processRequirement

s Analysis

Conceptual Design

Logical Design

Database Requirements

Conceptual Model

Implementation Model

* There is no universally accepted standard for either the design process or notation.

1. Entity-Relationship Modeling is a type of CDM

Entity Types

An entity type provides a description of the properties of entities in a domain

Relationships

Represents an association between two or more entity types.

Hemoglobin Myoglobin

ER modeling for HIV

ER models and fingerprints

ER models can be mapped onto relational tables.

String of attributes/properties that define and identify the relationship and are unique to the entity.

2. Unified Modeling Language (UML); another CDM

The standard object modeling language.

Notation is the class diagram which describes the attributes, operations, and relationships of a set of objects.

Class Diagram

UML versus ER

ER

ER was developed earlier for relational databases

ER uses keys: when one or more attributes of an entity are used to uniquely identify it

Uses relational tables

Not truly platform independent

UML

UML is object-oriented

Do not support keys

Not all relationships are given names or roles

Independent of platform

Building Useful Networks

Applications

Personalized Medicine?

Question 1.

True/False: Conceptual Data Models (CDMs) are only applicable to bioinformatics research.

Correct Answer: FALSE

Question 2.

Which of the following is not an activity in the design process for conceptual modeling?

a. Requirements Analysis

b. Conceptual Design

c. Conceptual Model

d. A. B. and C. are all examples of the design process.

e. All of the above and activities can vary as there is no universally accepted process or design.

Question 3.

Which of the following is FALSE in regards to Conceptual Data Models (CDMs)?

a. CDMs allow precise statements to made about the data.

b. CDMs are easier to read than to construct.

c. CDMs easily describe all data without including invalid data.

d. Entity Relationship and Unified Modeling Languages are types of CDMs

Thank you for your attention!

References and Images (In order of appearance)

- http://campus.murraystate.edu/academic/faculty/eweber/bio101/images/cell_to_dna_sm.jpg

- http://bioinfo.imdik.pan.pl/mediawiki/images/e/e1/Sek3.jpg

- http://asgpb.mhpcc.hawaii.edu/sequence/454sequencer.jpg

http://blog.chron.com/bakerblog/files/legacy/dna.jpg

http://www.nature.com/nature/journal/v464/n7289/images/464680a-i1.0.jpg

http://www.ornl.gov/sci/techresources/Human_Genome/home.shtml

http://25.media.tumblr.com/tumblr_loa5m3vYuO1qbh26io1_1280.jpg

http://www.sanger.ac.uk/about/history/hgp/

http://en.wikipedia.org/wiki/File:Myoglobin.png

http://en.wikipedia.org/wiki/File:1GZX_Haemoglobin.png

http://www.databaseanswers.org/data_models/hotels/index.htm

http://www.schillerlab.net/guides/hiv/image009.png

http://www.nature.com/scitable/content/6437/10[1].1073_pnas0701361104-fig2b_mid_1.jpg