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It is natural to try to place the new polynomial invariants of links in algebraic topology (e.g. to try to interpret them using homology or homotopy groups). However, one can think that these new polynomial invariants are byproducts of a new more delicate algebraic invariant of 3-manifolds which measures the obstruction to isotopy of links (which are homotopic). We propose such an algebraic invariant based on skein theory introduced by Conway (1969) and developed by Giller (1982) as well as Lickorish and Millett (1987). (This is the first paper I wrote about skein modules, almost 20 years ago. The recent survey of skein modules is available at http://arxiv.org/abs/math.GT/0602264.)
Józef H. Przytycki (Sun,) studied this question.