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The specific tools I use are Zotero (for citations, bookmarking, and note taking), EndNote (for citations and bibliographies), OpenOffice Writer (for note taking), and diigo (for bookmarking and annotations). I find I have to use both Zotero and EndNote because the latter handles lots of references (I have about 20,000) very well and because it integrates much better with my university's reference databases like CSA, EBSCO, or Science Direct, as well as with publishers' online databases and notification services like Blackwell Synergy. In general, I find EndNote much more "lightweight" (i.e., quicker to use and more responsive) than Zotero, but its integration with ordinary web documents and note-taking features are far weaker. I say "ordinary web documents" because most of the time with pdf files and other even slightly out of the ordinary web material (e.g., any of the U.S. Census Bureau's surveys), I have to enter the citation information manually. I use OpenOffice.org Writer to take notes involving mathematics, since it's much better for this than Zotero (or Word or EndNote). I use diigo to annotate and comment on web pages, including online pdf documents. None of the other tools comes close on this function.
One thing none of these packages does well is deal with web pages being displayed under a parent page. For example, if I use LexisNexis to retrieve newspaper articles, they appear as pdf files in a frame (I think it's a frame). Neither Zotero nor diigo gets the correct citation information, and neither EndNote nor OpenOffice Writer are designed even to try. I have to enter the bibliographic information manually, and I'm not even sure the URL will be reliable in Zotero or diigo since it points to the LexisNexis interface rather than to the individual newspaper article.
In any case, because no one application has all the functionality I need, I have some items' reference information in EndNote, Zotero, or diigo and notes in Zotero, EndNote, or as separate OO.o files. In addition, before using this set of
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The specific tools I use are Zotero (for citations, bookmarking, and note taking), EndNote (for citations and bibliographies), OpenOffice Writer (for note taking), and diigo (for bookmarking and annotations). I find I have to use both Zotero and EndNote because the latter handles lots of references (I have about 20,000) very well and because it integrates much better with my university's reference databases like CSA, EBSCO, or Science Direct, as well as with publishers' online databases and notification services like Blackwell Synergy.
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In any case, because no one application has all the functionality I need, I have some items' reference information in EndNote, Zotero, or diigo and notes in Zotero, EndNote, or as separate OO.o files. In addition, before using this set of tools I used Scribe and WikidPad.
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