Mai Nguyen BUS 550, Spring 2013 Dr. Minder Chen

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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). - PowerPoint PPT Presentation

Transcript of Mai Nguyen BUS 550, Spring 2013 Dr. Minder Chen

Conceptual data modeling for bioinformatics.

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 2013Dr. Minder Chen1Bioinformatics

the field of science in which biology, computer science, and information technology merge to form a single discipline. Biology (Source)DataInformation Processing and Systemhttp://campus.murraystate.edu/academic/faculty/eweber/bio101/images/cell_to_dna_sm.jpghttp://bioinfo.imdik.pan.pl/mediawiki/images/e/e1/Sek3.jpghttp://asgpb.mhpcc.hawaii.edu/sequence/454sequencer.jpg2Human Genome Projectidentify 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 DNAstore this information in databases,improve tools for data analysis,transfer related technologies to the private sector, andaddress the ethical, legal, and social issues (ELSI) that may arise from the project.

http://blog.chron.com/bakerblog/files/legacy/dna.jpghttp://www.nature.com/nature/journal/v464/n7289/images/464680a-i1.0.jpghttp://www.ornl.gov/sci/techresources/Human_Genome/home.shtml3Data Data Data Data,..

http://25.media.tumblr.com/tumblr_loa5m3vYuO1qbh26io1_1280.jpghttp://www.sanger.ac.uk/about/history/hgp/4Databaseshttp://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 2Attributes/propertiesThe design processRequirements AnalysisConceptual DesignLogical DesignDatabase RequirementsConceptual ModelImplementation Model

* There is no universally accepted standard for either the design process or notation.http://www.databaseanswers.org/data_models/hotels/index.htm71. Entity-Relationship Modeling is a type of CDMEntity 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.

HemoglobinMyoglobinhttp://en.wikipedia.org/wiki/File:Myoglobin.pnghttp://en.wikipedia.org/wiki/File:1GZX_Haemoglobin.png8ER modeling for HIV

http://www.schillerlab.net/guides/hiv/image009.png9ER models and fingerprintsER 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 CDMThe standard object modeling language.Notation is the class diagram which describes the attributes, operations, and relationships of a set of objects.

Class DiagramUML versus ERERER was developed earlier for relational databasesER uses keys: when one or more attributes of an entity are used to uniquely identify itUses relational tablesNot truly platform independentUMLUML is object-orientedDo not support keysNot all relationships are given names or rolesIndependent of platformBuilding Useful Networks

http://www.nature.com/scitable/content/6437/10[1].1073_pnas0701361104-fig2b_mid_1.jpg14Applications

Personalized Medicine?

Question 1.True/False: Conceptual Data Models (CDMs) are only applicable to bioinformatics research.

Correct Answer: FALSEQuestion 2.Which of the following is not an activity in the design process for conceptual modeling?Requirements AnalysisConceptual DesignConceptual ModelA. 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.

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 CDMsThank you for your attention!References and Images (In order of appearance)http://campus.murraystate.edu/academic/faculty/eweber/bio101/images/cell_to_dna_sm.jpghttp://bioinfo.imdik.pan.pl/mediawiki/images/e/e1/Sek3.jpghttp://asgpb.mhpcc.hawaii.edu/sequence/454sequencer.jpghttp://blog.chron.com/bakerblog/files/legacy/dna.jpghttp://www.nature.com/nature/journal/v464/n7289/images/464680a-i1.0.jpghttp://www.ornl.gov/sci/techresources/Human_Genome/home.shtmlhttp://25.media.tumblr.com/tumblr_loa5m3vYuO1qbh26io1_1280.jpghttp://www.sanger.ac.uk/about/history/hgp/http://en.wikipedia.org/wiki/File:Myoglobin.pnghttp://en.wikipedia.org/wiki/File:1GZX_Haemoglobin.pnghttp://www.databaseanswers.org/data_models/hotels/index.htmhttp://www.schillerlab.net/guides/hiv/image009.pnghttp://www.nature.com/scitable/content/6437/10[1].1073_pnas0701361104-fig2b_mid_1.jpg

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