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I always used a single babel.bib BibTex file to keep a record of all my readings. Great. Then I managed it using a VCS (first SVN, then git). Super great. But at the same time, resources like CiteUlike or Mendeley (but also other services like orcid) allow for cloud-like services of having this data everywhere, anytime. Super super great!

But this fails if you have no connection to internet (remote conference, ...) or more importantly if these services change their policy (mendeley to citeulike sync disappeared at a sudden). The work you provide is not yours. These are mostly commercial services while all the open-source tools are there. Most importantly, the multiplicity of tools makes it difficult to share bibliographic data easily, while if we would have a tool to translate between them this would make it possible (without changing your habits).

As a consequence, I wish to build such a "BibCloud" service with the following features:

  • bibcloud init : use with biblatex (but a format using bibjson is possible)
  • CLI coded in python (widespread in the scientific community), all databases + configuration files being stored in plain text files.
  • bibcloud commit -am' adding Sawyer14nature'; bibcloud push : CVS integration (git / hg / ...) - and storage in remote repositories (github, bitbucket)
  • bibcloud pull citeulike, bibcloud push citeulike : easy conversion + pull and push to existing accounts (Citeulike, Mendeley) - including synchronization of PDFs
  • bibcloud detect_dups records implementation of tools to detect and merge duplicate records, and duplicate fields (like bibcloud detect_dups authors: an author with different versions, like eg Tom Sawyer, T Sawyer, T J Sawyer or for journal names with bibcloud detect_dups journals)
  • bibcloud pull 2323422.pdf scan a pdf to extract its metadata (like the DOI) - allow to include the citation in the paper bibcloud push 2323422.pdf to simply send a file to colleagues.
  • bibcloud citekey Sawyer14 : generate a citekey according to a given rule
  • bibcloud edit Sawyer14 : edits one particular entry
  • bibcloud file Sawyer14 : files the PDF corresponding to the entry according to some rule
  • bibcloud push html easy conversion to some web format (github pages?) to read papers online.

Before attempting to put that together, I wish to know of the existing pieces the community may know.

Notes:

  • it is different from this question "Workflow for managing references?" as existing solutions like zotero or do not work for me. I wish to get the pieces of the puzzle together to build a command-line tool for managing bibliographies.
  • it is different to this question or to this other as they ask more for a GUI solution.
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  • I use dropbox to store my files + jabref to manage the references. I don't use CVS so I don't know how well it integrates, and I don't know if it can automatically parse a PDF, but it might be an option ;)
    – hugovdberg
    Commented Mar 20, 2014 at 14:11
  • You might take a look at refbase.net, aigaion.sf.net, bibsonomy.org or this wikipedia list: en.wikipedia.org/wiki/…
    – matth
    Commented Mar 20, 2014 at 14:15
  • @matth : I was all these web-based tools but my quest is more to provide a commandline tool (I edited the question to clarify that, thanks!)
    – meduz
    Commented Mar 20, 2014 at 14:35
  • a nice post related to the question: xcorr.net/2014/04/02/keeping-up-with-the-scientific-literature/…
    – meduz
    Commented Apr 7, 2014 at 12:57
  • I too came looking for such a thing.
    – Richard
    Commented Jan 23, 2015 at 2:00

1 Answer 1

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I think that you could use cloud reference manager's APIs, such as Mendeley APIs (http://apidocs.mendeley.com). I'd simply "wrap" corresponding RESTful APIs into a command-line interface (of course, APIs should provide needed granularity of functionality).

In regard to your concerns about loss of Internet connectivity and ownership of your data, these issues can be solved, correspondingly, by 1) enabling offline mode via cloud service's synchronization APIs (where available) and 2) mirroring service's proprietary local database to local open source database via export APIs (where available).

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    @Adam: Thank you, much appreciated! I'm a complete newbie in the TeX world, but my desire to do my best at creating reproducible Ph.D. dissertation materials pushed me toward joining this nice community. Commented Mar 21, 2014 at 15:59

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