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Re: [O] Managing articles in orgmode and collaboration

From: Christoph Groth
Subject: Re: [O] Managing articles in orgmode and collaboration
Date: Tue, 23 Sep 2014 15:14:00 +0200
User-agent: Gnus/5.13 (Gnus v5.13) Emacs/24.4.50 (gnu/linux)

Jorge A. Alfaro-Murillo wrote:

Perhaps I am biased because I learned LaTeX and BibTeX before Org, but I think that for references BibTeX (plus a little bit of emacs configuration) has everything I could need. I guess if you are more used to Org, it might be worth to invest time and come up with a org-based solution. Please keep us posted, I find this a very interesting thread.

This is an update about my experiments so far. Please comment! This is my current setup:

All the articles (mostly PDF files) are kept in one directory. There’s also an index.org file in there with headlines like this

--8<---------------cut here---------------start------------->8---
** [[file:vazifeh13-electromagnetic_response_weyl.pdf][Electromagnetic Response of Weyl Semimetals]]
:TITLE:    Electromagnetic Response of Weyl Semimetals
:BTYPE:    article
:ID:       vazifeh13-electromagnetic_response_weyl
:AUTHOR:   Vazifeh, M. M. and Franz, M.
:JOURNAL:  Phys. Rev. Lett.
Some comments/notes with links and in-line formulas.
--8<---------------cut here---------------end--------------->8---

These entries are created by org-bibtex-yank, Emacs’ bibtex is configured to generate the unique IDs (authorYY-three_first_words should be sufficiently unique in practice).

This setup works pretty well:

- Adding new articles is easy (there's still ample room for improvement). - Opening associated the associated article files and other links works well. - It’s easy to add notes (with in-line maths!) and do simple searches. - Linking from and to other org files (agenda, project-specific notes) is possible. - Additional attachment files (e.g. whiteboard photos from a discussion) can added with org-attach. - org-bibtex provides support to put entries into project-specific bibtex files (org-bibtex-export-to-kill-ring). - Thanks to the non-random unique IDs, it’s possible to jump to articles in the library from references in latex files, even if the key scheme in the latex file differs from the one used in index.org.

But not all is good:

- Scaling: Some simple tests seem to indicate that org mode becomes too sluggish with files of about 50k lines. This is a dimension that could be easily reached over 10 years if the file grows by 20 lines per day on average. This is not a problem in the beginning, but if the scheme does not scale to a few thousand entries, this renders the whole idea way less interesting.

- More advanced searching is lacking: AFAIK org mode currently does not support searching for articles of a given author that also contain a given keyword in the notes.

Any insights about these two problems? Perhaps the scaling could be managed by splitting index.org into several files (by year for example). But how to search then? It's probably not a good idea to add all the bibliography org-files into the agenda. (Is there a way to have a secondary list of agenda files?) Perhaps the solution for both problems would be to write a fast commandline query tool for such org-databases? The tool could even use a fast cache if necessary.

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