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Assignment #1

Assignment #1.

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Assignment #1

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  1. Assignment #1 Think about what you have learned about molecular structure not just from a purely scientific perspective, but from a conceptual perspective. What concepts and associated relationships would you need to capture to create a database or data structure to retrieve data on anybiomolecular structure (e.g. protein, DNA, RNA, peptide, carbohydrate, lipid, drug)? An important aspect of systems biology is the ability to place singular concepts in the broader functional context of a system. What concepts (attributes) and relationships would you need to completely represent the interactions among these molecules (e.g. protein-protein, protein-DNA, protein-RNA, enzyme-metabolite, receptor-peptide, protein-drug)? In bioinformatics, it is also very important to be aware of the existing data sources available. There is a wealth of valuable public data available in the broadly used databases (e.g. PDB, GenBank, KEGG) as well as more sub-field-specific databases (e.g. BioPD, HMDB, DrugBank, DIP). Research the existing public data sources that are relevant for the concepts and relationships you’ve come up with. Present your concepts as a diagram of boxes, including attributes of each concept and relationships between concepts – in this way you will have constructed a conceptual schema. Annotate your diagram with references to the public data sources you researched. It is up to you to determine how to best structure this schema. Feel free to use whatever tools you want to complete this assignment. You could even draw diagrams by hand. A couple of tools that might be useful are: Dia: http://live.gnome.org/Dia yED: http://www.yworks.com/en/products_yed_about.html PHAR201 Assignment 1 2012

  2. Assignment #1- Example Secondary Structure _type _ attributes is_part_of is_part_of is_part_of Helix _type _attributes RNA _type _attributes DNA _type _attributes Points will be awarded for the number of concepts (boxes) you include and the number of attributes associated with each concept PHAR201 Assignment 1 2012

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