Data Science in Omics Introduction

An OMICS Course Part 1: Shell, Organizing and Genomics

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Data Entry and Storage

Assignment

Learning Objectives

Following this assignment students should be able to:

  • understand the basic rules of tidy data
  • implement quality control for data entry in spreadsheets
  • create an SQL database by importing data

Reading

Lecture Notes

  1. Course Introduction
  2. Tidy Data
  3. Data Entry
  4. Demo Code for Where Students Can Get in the Course

Exercises

  1. Improving Messy Data (50 pts)

    A lot of real data isn’t very tidy, mostly because most scientists aren’t taught about how to structure their data in a way that is easy to analyze.

    Download a messy version of some of the Portal Project data. Note that there are multiple tabs in this spreadsheet.

    Think about what could be improved about this data. In a text file (to be turned in as part of the assignment):

    1. Describe five things about this data that are not tidy and how you could fix each of those issues.

    2. Could this data easily be imported into a programming language or a database in its current form?

    3. Do you think it’s a good idea to enter the data like this and clean it up later, or to have a good data structure for analysis by the time data is being entered? Why?

  2. Data entry validation in Excel (50 pts)

    You’re starting a new study of small mammals at the NEON site at Ordway-Swisher. Create a spreadsheet in Excel for data entry. It should have four columns: Year, Site, Species, and Mass.

    Set the following data validation criteria to prevent any obviously wrong data from getting entered:

    1. Year must be an integer between 2015 and 2025.
    2. Site should be one of the following A1, A2, B1, B2.
    3. Species should be one of the following Dipodomys spectabilis, Dipodomys ordii, Dipodomys merriami.
    4. Mass should be a decimal greater than or equal to zero but less than or equal to 500 since mass is measured in grams in this study and nothing bigger than half a kilogram will possibly fit into your Sherman traps. Change the error message on this validation criteria to explain why data is invalid and what the valid values are.

    Save this file as yourname_ordway_mammal_data.xlsx.