How to organise bookmarks?

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Use the structure

Merge with existing structure

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Infer an initial structure

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Study cases

del.icio.us

Study the literature

Margaret E.I. Kipp and D. Grant Campbell - Patterns and Inconsistencies in Collaborative Tagging Systems

S. A. Golder, B. A. Huberman - The Structure of Collaborative Tagging Systems

C. Marlow et al. - HT06, Tagging Paper ...

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P. Merholz - Metadata for the masses