From Files to Database

Figure 1:   From Files to Database



      Data management is usally a big challenge for the project of long-term aim. The risks rise up along with the giant-amount data generation and the following data clean, organization, store, sharing, security, and mining. Excel or notepad is a popular but low-effort way for many existing biomedical projects to record the data. Consequently, more and more projects turn to more efficient MySQL database. To our knowledge, the comparison between excel and Mysql database is listed below.


Table 1:   Excel Files vs. MySQL database
Excel MySQL MySQL Advantage
Access Location Local Machine Internet Share Easier for remote sharing
Data Source Multiple Copies on different machines Single Data Source Easier for Data Version Control and Maintenance
Data Input Slow and wrong-input risk Quick and Standard Input 1)Validate User’s Input
2)Allow Batch input
Access Permission Control Weak Strong Multi-layers access protections
View Change History None Possible Information Change History is Recorded
Unexpected Information Deletion Can't recovered Can be recovered Important information can be protected from deletion
Data Backup None Automatic Periodic Data Backup Avoid Data Missing
Data Summary Weak Strong Good for Data Visualization


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  Allergy Database Design

      The database of UT Southwestern Allergic Disease and Antiviral Responses Program will contain three layers of datab including Patients layer, Samples layer, and Experiments layer. Inside patients layer, clinical information such as personal identifier, chemotherapy, followup, diagnosis, and others. Samples layer records the details of sampling. Experiments layer contains the experiments on samples and experimental processed results. Below please find the brief achitect.


Figure 2:   Achitect of Database Design



      The design of database contains a serial of considerations such as

  1. Data Quick Query
  2. Least Data Redundancy
  3. Variable Codebook for standardize Data Input


      Quantitative Biomedical Research Center (https://qbrc.swmed.edu) of UT Southwestern Medical Center has been working on database design and online biomedical softwares for more than five years. Our engineers have long-time work experiences for reliable database design and user-friendly web portal implement. One example is shown below.


Figure 3:   An Example of Our Previous Biomedical Database Structure



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  Database Usage

Data Input and Query

      An well-designed MySQL database is very powerful for data usage. Data query becomes a easy task and makes possible user-friendly web input and display.


Figure 4:   An Example of Our Designed Database Web Portal



      Inside allergy database, our preliminary experimental results has been well organized. Quick query is one of the most useful features based on MySQL database. For example,

Table 2:   Search on Skin Test Reactivity



Data Summary

      The power of web software development lets data summary be easier and clearer. Real-time data summary may help researchers dynamically understand the status of database.


Figure 5:   An Example of Real-time Patient Components

      

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  Database Security

      Data security is always on the top of our consideration. Under the strict data management and maintenance of UT Southwestern, we have developed multi-levels of data protection strategies, such physical isolation and data encryption.


Figure 6:   Data Security Strategies

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