1. A computer-implemented method performed by data processing apparatus comprising one or more computers in data communication, the method comprising: receiving publisher affiliation data for native applications that define, for each native application, an affiliated publisher for the native application; for each native application of a set of native applications, determining, based on the publisher affiliation data, whether the native application is affiliated with a publisher that provides content addressed by URIs determined for the native application; for only the native applications that are determined to be affiliated with a publisher that provides content addressed by URIs determined for the native application; selecting URIs based on the URI pattern for the native application; and indexing content accessible by the URI for the native application in an index that is searchable by a search engine.