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By standards, guidelines, and practices for collecting data I mean the rules that facilitate:

  • Practical value: Collecting data with a specific goal in mind
  • Data integrity: Minimizing omissions and biases
  • Infrastructure: Integrating the data into decision making

National census and household surveys meet these requirements, and so do other data collected by the federal government and universities.

Almost each agency has some guidelines for dealing with information. Examples:

My questions are:

  1. What are the standard references for these purposes?
  2. Have any standards been updated to account for big data, like for recording those NYC taxi trips or 311 calls?

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Civic Common's Open Data Guidelines seem to be the default reference for most standards that I'm aware of. It's important to point out that Civic Commons is not a government entity/agency, however everyone involved in the project that I am aware of works for/has worked for/works with government to see these guidelines come to life. There are some references to official government documents in the guidelines, which specifically are applicable to your question.
http://wiki.civiccommons.org/Open_Data_Guidelines/

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