Re: [Axiom-developer] Axiom bibliography

[Bob McElrath]

C Y address@hidden wrote:
> The problem of making a bibtex file into a pamphlet file is going to be
> a big one, primarily because in order to make some sense of the one
> (large) file it would be advisable to keep it ordered by date, author,
> or some other key.  But the only way I know of which might be able to
> achieve this would be to use some tool for the management of
> bibliographies.  JabRef would be far and away my preference - it is the
> leading open source solution that I am aware of, and I'm hoping its
> Groups feature could be used somehow to manage things:
> 
> http://jabref.sourceforge.net/
> http://jabref.sourceforge.net/images/Jabref-ScreenShot-MainWindow.png
> 
> but if we do use such a tool we have the problem of its being designed
> to work with bibtex, not bibtex in pamphlet :-/.

I'm working on a system for physicists which will require an extensive
reference database (at least all of the arXiv plus all of SPIRES) and
furthermore, I want wiki pages to actually link to the bibliography.

For physics anyway, search engines already exist to find papers and even
entire bibtex entries (via arXiv, SPIRES, and NASA ADS).  For math see
the Front here at UC-Davis which also provides bibtex:
http://front.math.ucdavis.edu/  AND these systems all provide a concise
identifier for each paper.  (e.g. math.AC/0604301)  Historic papers are
often more of a problem.

I have discussed this project a bit with Bill privately, but would
welcome more widespread development in this direction.

Right now I have an experimental Plone site (because of the existence of
the Bibliography Archetype -- same as Axiom Portal:
    http://portal.axiom-developer.org/bibliography_view
).  Maybe I have missed it but I do not see a way to search the
bibliography.  Furthermore when viewing a bibliography entry it does not
give you a concise identifier for each paper that you can \cite{},
unless you go export to bibtex, then examine the output.  

I would like to add search and \cite{} capability from wiki pages.  This
would allow discussion of papers, and even back-references on the wiki!
It would be super-sweet if the search could be done in a sidebar, next
to the edit window, using AJAX, so that you could retrieve the
identifier for \cite{} without having to open a new browser window.

> Has anyone any particular ideas on this?  For me the issue will become
> rapidly more concrete as I work on the Unit and Emacs pamphlets, both
> of which (units especially) are likely to have a healthy bibliography
> by the time they are "done".  Since this is a core design issue for the
> Axiom literate document system it needs discussion and consideration by
> all interested parties.  There are a LOT of papers to include even if
> you just take the ones on Axiom itself - when you branch out to other
> types of relevant programs (proof checkers, etc.) and then pure math in
> general we're talking THOUSANDS of papers which might (should) wind up
> being cited by Axiom.  Each pamphlet will include the specific papers
> it references of course, but the Bibliography as a whole would probably
> constitute a volume all by itself.  We'll need intelligent ways to
> merge, sort, and manage this process.  I guess I would propose this as
> a rough draft:
> 
> 1.  Create and maintain a central bibliography, starting with the
> Nelson Beebe axiom.bib file as a beginning.  Pamphlet authors would be
> encouraged to use the citations already present if they want to cite an
> existing paper.
> 
> 2.  Each new pamphlet will undoubtedly cite papers and other works not
> included in the main axiom.bib file.  They will most likely either
> append these new entries on to the end of axiom.bib or maintain a
> separate file.  When a new pamphlet is submitted to Axiom, part of the
> inclusion process will be incorporating the new bibliography entries
> into the main axiom.bib file.  This can be done either via a diff
> (preferably of an altered axiom.bib which has been sorted by whatever
> criteria we decide to organize the main file) or the inclusion of a bib
> file which contains all the new references.  In the latter case,
> someone with the correct tools can merge the new references into the
> main file.

I have been thinking to write a back-end which will interrogate other
search engines for bibtex, if someone enters something unknown.  For
instance, SPIRES references are easy to recognize by syntax (e.g.
McElrath:2005bp) same for arXiv (e.g. hep-ph/0506151) so the wiki system
can know which database to import from if it doesn't have the
bibliography entry already.

> 3.  We need some way to identify categories of paper within the main
> bib file - maybe some kind of agreed upon keywords for each category of
> paper.  This will evolve somewhat but most major categories should be
> agreed upon in advance.  This will allow someone looking for a
> particular paper to cite to quickly identify the relevant subset of the
> bib file.  This will require jabref or some similar tool to handle
> properly, but that is going to be unavoidable in such a large file.

Rather than explicitly identify categories, why not just use
backreferences?  e.g. a wiki page called CommutativeRings has a number
of references.  If you viewed one of those entires in the bibliography,
it would show "pages that cite this paper" including your
CommutativeRings.

> 4.  If things get too large, we might have to consider "group" based
> bib files - I don't know what the size limits are for bibtex but it
> must have some.

I say one huge database.  I know of no size limits.  If one wants to
process with latex one could always extract the subset of bibtex entries
from the database.

> 5.  IIRC there is some way to process bib files as TeX documents?  If
> so we can make the bibliography file available on the wiki like any
> regular pamphlet file.  I'll have to check that.

What do you mean here?  Have you seen the Axiom Portal bibliography that
I'm talking about?

If you're interested in working on this, please do!  For the near term
I'm trying to get an XHTML+XML plone site working, and developing a new
wiki syntax that is faux-latex and generates XHTML+MathML.  I have not
started on the bibliography stuff yet, but I will need some kind of
interface to query the bibliography.  e.g. "give me a formatted citation
or URL for the identifier McElrath:2005bp".  If you want to write that,
or look into it, please do!

For now the software I'm building on is the CMF Bibliography Archetype:
    http://plone.org/events/sprints/paderborn/BibliographyTeam

--
Cheers,
Bob McElrath [Univ. of California at Davis, Department of Physics]

    "It is almost universally felt that when we call a country
    democratic we are praising it; consequently, the defenders of every
    kind of regime claim that it is a democracy, and fear that they
    might have to stop using the word if it were tied down to any one
    meaning." -- George Orwell

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