Jabref is a free software than can save a bibliography in bibtex format. This format can be used to import citation in windows or latex based text editing system such as Lyx.
Link to PDF or other files
Jabref can automatically create links for files for which you have an entry, if they are located under the main file directory. To change the main file directory:
Options -> Preferences -> External programs -> Main file directory
But the main file directory can also be specified for each bibtex database under:
File -> Database properties -> General file directory and PDF directory
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