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The idea of using an ontology to enrich user queries with domain knowledge has attracted considerable attention from the database and KR communities during the last fifteen years or so. The ontology and the user query can be conveniently seen as two components of one composite query, called ontology-mediated query (omq), while an omq language (OL,QL) collects all such omqs where the ontology is expressed using the ontology language OL and the user query comes from the query language QL. The evaluation problem for rule-based omq languages of the form (OL,CQ), where OL is a rule-based ontology language, i.e., it collects ontologies modelled using tuple-generating dependencies (a.k.a. existential rules), and CQ is the language of conjunctive queries, has been extensively studied in the literature. In particular, the notion of first-order rewritability of such languages, i.e., the property of being able to rewrite every omq from the language in question to an equivalent first-order query, has been studied in depth. This research effort led an algorithmic characterization of when a rule-based omq language (OL,CQ) is first-order rewritable. More precisely, there is a uniform algorithm Rewrite such that, for every rule-based ontology language OL, the omq language (OL,CQ) is first-order rewritable iff for every omq O from (OL,CQ), the algorithm Rewrite on input O terminates and constructs a first-order rewriting of O. The question that we are interested in is whether the above algorithmic characterization can be extended to rule-based omq languages of the form (OL,nCQ), where nCQ is the language of conjunctive queries with the useful feature of negation. The goal of this work is to initiate effort towards the settlement of the above highly non-trivial question. To this end, we provide a new algorithm, which is a non-trivial extension of the algorithm Rewrite for positive omqs, and show the following: under the Skolem semantics, a well-established approach for defining the answer to a rule-based omq when the user query can use negation, the proposed algorithm is a first-order rewriter for (OL,nCQ), where OL is the language of linear or acyclic tuple-generating dependencies, two central rule-based ontology languages that ensure first-order rewritability for positive omqs. We strongly believe that the new algorithm can serve as a good starting point towards the full settlement of our main question.