1. Computational Biology Dr. Jens Allmer Lecture Slides Week 5

2. MBG404 Overview Data Generation Processing Storage Mining Pipelining

3. Database Management Systems

4. Company/ Organization Database Size (GB) DBMSSystem Arch. DBMS Vendor System Vendor Storage Vendor France Telecom 29,232OracleSMPOracleHP AT&T 26,269DaytonaSMPAT&TSun SBC 24,805TeradataMPPTeradataNCRLSI Anonymous 16,191 DB2 for Unix MPP/ ClusterIBM Amazon.com 13,001OracleSMPOracleHP Kmart 12,592TeradataMPPTeradataNCRLSI Claria Corporation 12,100OracleSMPOracleSunHitachi Health Insurance Review Agency 11,942Sybase IQClusterSybaseHPHitachi FedEx Services 9,981TeradataMPPTeradataNCREMC Vodafone D2 GmbH 9,108TeradataMPPTeradataNCRLSI

5. Database Management Systems Physical Schema Conceptual Schema View 1View 2View 3 DB Users

6. Database Management Systems

7. A Relation is a Table Attributes (column headers) Tuples (rows) Contains data -> Instance Domain All possible values namemanf Winterbrew Bud Lite Pete’s Anheuser-Busch Beers

8. Schemas Relation schema = relation name and attribute list. –Optionally: types of attributes. –Example: Beers(name, manf) or Beers(name: string, manf: string) Database = collection of relations. Database schema = set of all relation schemas in the database. Instance of a relation = a table in a database with data

9. Anomalies Goal of relational schema design is to avoid anomalies and redundancy. –Update anomaly : one occurrence of a fact is changed, but not all occurrences. –Deletion anomaly : valid fact is lost when a tuple is deleted.

10. Example of Bad Design Drinkers(name, addr, beersLiked, manf, favBeer) nameaddrbeersLikedmanffavBeer JanewayVoyagerBudA.B.WickedAle Janeway???WickedAlePete’s??? SpockEnterpriseBud???Bud Data is redundant, because each of the ???’s can be easily figured out.

11. This Bad Design Also Exhibits Anomalies nameaddrbeersLikedmanffavBeer JanewayVoyagerBudA.B.WickedAle JanewayVoyagerWickedAlePete’sWickedAle SpockEnterpriseBudA.B.Bud Update anomaly: if Janeway is transferred to Intrepid, will we remember to change each of her tuples? Deletion anomaly: If nobody likes Bud, we lose track of the fact that Anheuser-Busch manufactures Bud.

12. 1st Normal Form All attributes need to be atomic

13. 2nd Normal Form Must be in 1st NF a key must uniquely identify each tuple

14. 3rd Normal Form Must be in 2nd NF attributes not part of a key must directly depend on one of the keys

15. One-One Relationships In a one-one relationship, each entity of either entity set is related to at most one entity of the other set. Example: Relationship Best-seller between entity sets Manfs (manufacturer) and Beers. –A beer cannot be made by more than one manufacturer, and no manufacturer can have more than one best-seller (assume no ties).

16. Many-One Relationships Some binary relationships are many-one from one entity set to another. Each entity of the first set is connected to at most one entity of the second set. But an entity of the second set can be connected to zero, one, or many entities of the first set.

17. Many-Many Relationships Focus: binary relationships, such as Sells between Bars and Beers. In a many-many relationship, an entity of either set can be connected to many entities of the other set. –E.g., a bar sells many beers; a beer is sold by many bars.

18. End Theory I 5 min mindmapping 10 min break

19. Practice I

20. MS Access Create new Tables: –Plant –Features –FeatureTypes

21. Create a Table

23. Edit a Table

24. Create the Three Tables Plant Features FeatureTypes

25. Add Attributes Plant –ID –Gender –Species –Strain –Clone

26. Add Attributes Features –ID –FeatureType –Value

27. Add Attributes Features –ID –Type –Unit

28. Table Space

29. Notice

30. More Editing

32. Notice

33. Fill with Data Import the data in the plants.csv file

34. Select Appropriate table

35. Some adjustments Are needed here

36. Need to name the Columns appropriately

37. Insert Data Import Feature table Import features txt file

38. Real Data Download GO Terms: –http://archive.geneontology.org/latest-termdb/go_daily- termdb.obo-xml.gzhttp://archive.geneontology.org/latest-termdb/go_daily- termdb.obo-xml.gz Change file extention to.xml so that Access can import Import file into Access –May take a short while –Errors will occur (we ignore them for now) Have a look at the tables Analyze the relationships (were they imported?)

39. End