C# Regex Split – everything inside square brackets

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Split won’t help you here; you need to use regular expressions:

// using System.Text.RegularExpressions;
// pattern = any number of arbitrary characters between square brackets.
var pattern = @"\[(.*?)\]";
var query = "H1-receptor antagonist [HSA:3269] [PATH:hsa04080(3269)]";
var matches = Regex.Matches(query, pattern);

foreach (Match m in matches) {
    Console.WriteLine(m.Groups[1]);
}

Yields your results.

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