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"To obtain deeper insight into lignin biosynthesis and the metabolic network it is embedded in, we used a systems biology approach as defined by Ideker et al"

In this sentence, I'm confused about the clause-- "it is embedded in", is it an attributive clause?

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    It's a relative clause with locative meaning, in which it is embedded. – KarlG Jun 2 '18 at 13:32
  • It's a 'bare' relative clause, where the relativised element is missing but understood as complement of the locative preposition "in", i.e. "in x", where x represents the missing relativized element, which has the nominal "metabolic network" as antecedent. – BillJ Jun 3 '18 at 7:58
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Yes, it is a relative clause. Grammatically, it would be correct to say:

(1) "To obtain deeper insight into lignin biosynthesis and the metabolic network that it is embedded in, we used a systems biology approach as defined by Ideker et al"

or

(2) "To obtain deeper insight into lignin biosynthesis and the metabolic network which it is embedded in, we used a systems biology approach as defined by Ideker et al"

or

(3) "To obtain deeper insight into lignin biosynthesis and the metabolic network in which it is embedded, we used a systems biology approach as defined by Ideker et al"

But there is a problem, and this might be the source of your confusion--is biosynthesis a thing that can be embedded? Is this how we think of biosynthesis? Biosynthesis is a process that is not independent of its environment.

A better statement might be:

(4) "To obtain deeper insight into lignin biosynthesis and the metabolic network in which it functions, we used a systems biology approach as defined by Ideker et al"

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