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A geodatabase doesn't provide much flexibility in organizing your data hierarchically. All feature sets live either at the top level of the database, or one level down in feature datasets. A feature dataset can't, in turn, contain another dataset. I'm interested in hearing how others organize their data, especially in environments where they must use a geodatabase and are stuck with these limitations.

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Enterprise Geodatabase (ArcSDE) support Versioning… – Mapperz Jun 29 '12 at 21:11
up vote 6 down vote accepted

Typical organization methods that I've seen are by prefixing. In an enterprise geodatabase, this can be done with an owner/schema name (e.g. UTIL.WMETER or by prefixing the featureclass/table name itself with a prefix string, then underscore, then name UTIL_WMETER). Prefixing the featureclass/table name also works in personal/file geodatabases.

Because of editing overhead for feature datasets, they aren't usually used as a primary organizational mechanism.

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