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I use the online tool citeulike to manage my bibliography. The main tool to organize the library is tags (functionally equivalent to tags here on this site). One problem I seem to be having is I do a very poor job of initially choosing tags, so I need to continually re-tag my library to keep it organized.
Is there any advice on choosing an intitial set of tags? Or will it be necessary for me to continually maintain my library to keep it organized/updated as much as I would like?
Tagging is only useful if you use it with discipline. Look at Wikipedia or Stackexchange, most articles can be determined by 5-6 categories (science - math - geometry - euclidean geometry - metric). Stackexchange has a max. of 5 tags, often you only see 1-2 on questions, which is often pointless, as those tags will appear often in the question/paper title and abstract too. Wasted time.
So, if you decide to create a tagging system, use at least 4-6 tags depending on how interdisciplinary and specialized your paper/link collection is.
Also consider to not only tag by topic but also kind (review, letter, peer-reviewed, experimental results, theoretical analysis, explanation of new measurement method, meta-discussion...), year, personal rating (very interesting article you learned a lot from and should read again from time to time), rarely/often/top cited, new theory/model, strongly discussed in the research community
A last note. I use myself Copernic Desktop Search as a supplementary tool, I download all papers of possible interest (disk space is cheap ;) ), papers I read, will read or maybe will never take a look at. The point is that Desktop Search software often has more powerful search operators and sorting mechanisms than Google Scholar & Co. If you know how to use them, you can save a lot reading and tagging time or tagging at all. You know, if you are smart in using Google & search operators and have a good vocabulary, you don't have to ask a lot questions on internet boards.
Conclusion:
Don't use tagging for creating a pure thematic and linear directory structure, if finding again your papers or bits of information can be done by learning a good Desktop Search software. Use your tags in a personal way and remember, the point is not to structure your bibliography like a folder directory for categorized files, the point is to find again the bits of knowledge and most memorable papers, which will rather look like a strongly interconnected nonlinear tag cloud. If you look how people tag sites on del.ic.ious, often only 2 or 3 tags, sometimes using up to 10 pure thematic redundant tags, they are doing it imho wrong and waste a lot of time.
I don't use citeulike myself, but I think it's important to make a difference between tags and keywords. Indeed, keywords are usually already included in the paper or at least in the abstract, so you don't need to retag them with duplicate information. Instead, it's better to use tags to give some personal context, such as why did you read this paper in the first place, or which general idea can you connect it to, or for which of your papers you used it, etc. In this case, there is no "wrong" or "right" tag, just some facts.
The best solution of my is Papers from mekentosj. I should also mention that using tags is not an efficient solution for me; at the tagging moment I could not think about relevant tags and later I would not be able to find the paper. In my system I organized papers in collections (like folders) and search for them using keywords (like one would on in Web of Science) or authors or any other usual field.
One of the great things about CiteULike is that you can see what papers you have in common with other people, and what they're tagging them as. That can give you a good clue when you're starting tagging.
However, whatever you choose, it will evolve as you aggregate a larger and larger library of references, so don't be afraid to keep it flexible.
In the end, your tagging system will be unique to you, because your interests are unique. For example, in my library, I've got a medical-epidemiology tag, because that covers around 1% of my library. If I had no such papers, it would be a useless tag. If I were doing medical epidemiology research, it would also be a useless tag, because I'd have to apply it to 90+% of my library.
Learn by your own experience: how do you use tags? Which tags have helped you find things? Which tags have you used to try to find things, that turned out to be dead ends?
sequence analysis) and some exactly related to your projects (with their names)? Then, after some time, you can search either for its general content (it was about X) or by your former project (I used it for Y). Does it seems OK? (I like tags and tagging but I cannot say much besides that redundancy is often usefull; e.g. for my delicious account I use typically 5 tags per webpage).