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What would be the best way to insert metadata into a database that need to be logicaly connected files that are stored locally on a web-server?

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In general, databases control their own storage. The proper procedure is to load data into tables in the database. This is important, because databases manage storage and memory. In a typical configuration, you don't want to be accessing files being updated by another application. And, you typically don't want to be storing database data over the network.

The general answer to the question is that you want to load data into the database.

That said, many database engines allow you to remotely access data in other databases or through a technology such as ODBC. You can get drivers for flat files, even those stored remotely on the network. However, this is not an optimal set up for querying. Alternatively, databases can be used to manage metadata for remote files, such as image files stored on disk. The purpose is to allow searches through the metadata which, in essence, retrieve file names that are then resolved (either on the client side or server side, depending on the architecture).

You should, perhaps, ask another question with a lot more detail about what you are trying to accomplish and about which database you are using.

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