18
$\begingroup$

Background

I am overseeing the input of data from primary literature into a database. The data entry process is error prone, particularly because users must interpret experimental design, extract data from graphics and tables, and transform results to standardized units.

Data are input into a MySQL database through a web interface. Over 10k data points from > 20 variables, > 100 species, and > 500 citations have been included so far. I need to run checks of the quality of not only the variable data, but also the data contained in lookup tables, such as the species associated with each data point, the location of the study, etc.

Data entry is ongoing, so QA/QC will need to be run intermittently. The data have not yet been publicly released, but we are planning to release them in the next few months.

Currently, my QA/QC involves three steps:

  1. a second user checks each data point.
  2. visually inspect histogram each variable for outliers.
  3. users report questionable data after spurious results are obtained.

Questions

  1. Are there guidelines that I can use for developing a robust QA/QC procedure for this database?
  2. The first step is the most time consuming; is there anything that I can do to make this more efficient?
$\endgroup$
25
$\begingroup$

This response focuses on the second question, but in the process a partial answer to the first question (guidelines for a QA/QC procedure) will emerge.

By far the best thing you can do is check data quality at the time entry is attempted. The user checks and reports are labor-intensive and so should be reserved for later in the process, as late as is practicable.

Here are some principles, guidelines, and suggestions, derived from extensive experience (with the design and creation of many databases comparable to and much larger than yours). They are not rules; you do not have to follow them to be successful and efficient; but they are all here for excellent reasons and you should think hard about deviating from them.

  1. Separate data entry from all intellectually demanding activities. Do not ask data entry operators simultaneously to check anything, count anything, etc. Restrict their work to creating a computer-readable facsimile of the data, nothing more. In particular, this principle implies the data-entry forms should reflect the format in which you originally obtain the data, not the format in which you plan to store the data. It is relatively easy to transform one format to another later, but it's an error-prone process to attempt the transformation on the fly while entering data.

  2. Create a data audit trail: whenever anything is done to the data, starting at the data entry stage, document this and record the procedure in a way that makes it easy to go back and check what went wrong (because things will go wrong). Consider filling out fields for time stamps, identifiers of data entry operators, identifiers of sources for the original data (such as reports and their page numbers), etc. Storage is cheap, but the time to track down an error is expensive.

  3. Automate everything. Assume any step will have to be redone (at the worst possible time, according to Murphy's Law), and plan accordingly. Don't try to save time now by doing a few "simple steps" by hand.

  4. In particular, create support for data entry: make a front end for each table (even a spreadsheet can do nicely) that provides a clear, simple, uniform way to get data in. At the same time the front end should enforce your "business rules:" that is, it should perform as many simple validity checks as it can. (E.g., pH must be between 0 and 14; counts must be positive.) Ideally, use a DBMS to enforce relational integrity checks (e.g., every species associated with a measurement really exists in the database).

  5. Constantly count things and check that counts exactly agree. E.g., if a study is supposed to measure attributes of 10 species, make sure (as soon as data entry is complete) that 10 species really are reported. Although checking counts is simple and uninformative, it's great at detecting duplicated and omitted data.

  6. If the data are valuable and important, consider independently double-entering the entire dataset. This means that each item will be entered at separate times by two different non-interacting people. This is a great way to catch typos, missing data, and so on. The cross-checking can be completely automated. This is faster, better at catching errors, and more efficient than 100% manual double checking. (The data entry "people" can include devices such as scanners with OCR.)

  7. Use a DBMS to store and manage the data. Spreadsheets are great for supporting data entry, but get your data out of the spreadsheets or text files and into a real database as soon as possible. This prevents all kinds of insidious errors while adding lots of support for automatic data integrity checks. If you must, use your statistical software for data storage and management, but seriously consider using a dedicated DBMS: it will do a better job.

  8. After all data are entered and automatically checked, draw pictures: make sorted tables, histograms, scatterplots, etc., and look at them all. These are easily automated with any full-fledged statistical package.

  9. Do not ask people to do repetitive tasks that the computer can do. The computer is much faster and more reliable at these. Get into the habit of writing (and documenting) little scripts and small programs to do any task that cannot be completed immediately. These will become part of your audit trail and they will enable work to be redone easily. Use whatever platform you're comfortable with and that is suitable to the task. (Over the years, depending on what was available, I have used a wide range of such platforms and all have been effective in their way, ranging from C and Fortran programs through AWK and SED scripts, VBA scripts for Excel and Word, and custom programs written for relational database systems, GIS, and statistical analysis platforms like R and Stata.)

If you follow most of these guidelines, approximately 50%-80% of the work in getting data into the database will be database design and writing the supporting scripts. It is not unusual to get 90% through such a project and be less than 50% complete, yet still finish on time: once everything is set up and has been tested, the data entry and checking can be amazingly efficient.

$\endgroup$
  • 4
    $\begingroup$ Well, I'm pretty much in love with this answer. I would like the emphasize that, in following point 4, you should keep the checks simple - there are often little incongruities in real data that your entry-folks should be able to enter but which you won't be able to foresee. For example, I make sure that dates are entered as dates; but I've stopped having hard rules about date ranges, and instead check that with reports, and follow up out-of-bounds values with whomever did the data entry. $\endgroup$ – Matt Parker Feb 22 '11 at 5:42
  • 5
    $\begingroup$ Preventing someone from entering a value that they believe to be right can introduce more error than detecting and investigating it. $\endgroup$ – Matt Parker Feb 22 '11 at 5:43
  • $\begingroup$ +1, great answer. I agree with Matt, I too love this answer:) $\endgroup$ – mpiktas Feb 22 '11 at 7:51
  • 1
    $\begingroup$ @Matt Good points, both of them. I completely agree. Concerning the first one, a good approach is to test the data entry procedures on a small representative subset of the data and thoroughly go over all the issues that arise. This won't address everything that can possibly come up, but it identifies most major issues early on and lets you deal with them effectively. $\endgroup$ – whuber Feb 22 '11 at 14:44
  • 2
    $\begingroup$ Adding as this information is useful in one place. 1. Create a business rules document that contains the meta data. including the rules used to produce derived variables such as age. 2. If this is an administrative database in particular, assume that variables will change over time, e.g. new codes are added. In the metadata, explain when the change occurred, and how this may affect any time series work. 3. If the database will be added to over time, date and time stamp changes to the database. $\endgroup$ – Michelle Jan 22 '12 at 6:43
3
$\begingroup$

DataOne provides a helpful set of data management best practices that can be filtered by tag. The best practices tagged with "quality", found at http://www.dataone.org/best-practices/quality, reiterating and expanding on many of the points made by @whuber. Here is a list of the topics covered there (in alphabetical order):

  • Communicate data quality
  • Confirm a match between data and their description in metadata
  • Consider the compatibility of the data you are integrating
  • Develop a quality assurance and quality control plan
  • Double-check the data you enter
  • Ensure basic quality control
  • Ensure integrity and accessibility when making backups of data
  • Identify outliers
  • Identify values that are estimated
  • Provide version information for use and discovery
$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.