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Mai Nguyen BUS 550, Spring 2013 Dr. Minder Chen

Conceptual data modeling for bioinformatics. Erich Bornberg -Bauer and Norman W. Paton. (2002). Briefings in Bioinoformatics . Vol. 3. No. 2. 166-180. Mai Nguyen BUS 550, Spring 2013 Dr. Minder Chen. Bioinformatics. Data. Information Processing and System. Biology (Source).

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Mai Nguyen BUS 550, Spring 2013 Dr. Minder Chen

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  1. Conceptual data modeling for bioinformatics.Erich Bornberg-Bauer and Norman W. Paton. (2002). Briefings in Bioinoformatics. Vol. 3. No. 2. 166-180. Mai Nguyen BUS 550, Spring 2013 Dr. Minder Chen

  2. Bioinformatics Data Information Processing and System Biology (Source) …the field of science in which biology, computer science, and information technology merge to form a single discipline.

  3. 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.

  4. Data Data Data Data,…..

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

  6. 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. Attributes/properties Entity 2 Entity 1 *A type of notation that describes entity types and relationships.

  7. The design process Requirements Analysis * There is no universally accepted standard for either the design process or notation. Database Requirements Conceptual Design Conceptual Model Logical Design Implementation Model

  8. 1. Entity-Relationship Modeling is a type of CDM Entity Types Relationships Represents an association between two or more entity types. • An entity type provides a description of the properties of entities in a domain Hemoglobin Myoglobin

  9. ER modeling for HIV

  10. 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.

  11. 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.

  12. Class Diagram

  13. UML versus ER ER UML UML is object-oriented Do not support keys Not all relationships are given names or roles Independent of platform • 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

  14. Building Useful Networks

  15. Applications

  16. Personalized Medicine?

  17. Question 1. • True/False: Conceptual Data Models (CDMs) are only applicable to bioinformatics research. Correct Answer: FALSE

  18. Question 2. • Which of the following is not an activity in the design process for conceptual modeling? • Requirements Analysis • Conceptual Design • Conceptual Model • A. B. and C. are all examples of the design process. • All of the above and activities can vary as there is no universally accepted process or design.

  19. Question 3. • Which of the following is FALSE in regards to Conceptual Data Models (CDMs)? • CDMs allow precise statements to made about the data. • CDMs are easier to read than to construct. • CDMs easily describe all data without including invalid data. • Entity Relationship and Unified Modeling Languages are types of CDMs

  20. Thank you for your attention!

  21. 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

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