Re: [NTG-context] Bibliographic Databases

2008-04-21 Thread Dietrich Rordorf / MDPI
Hi All,

Why not try an existing, online tool.? There are severals, most of them 
support export to various formats, e.g. BibTeX, RIS, EndNote, etc.. Some 
of them have a Word plug-in, too.

http://www.connotea.org/
Free online reference management tool for scientists
Nature Publishing Group

http://www.citeulike.org/
Free online reference management tool for scientists
Oversity Ldt.

http://www.bibsonomy.org/
Free online reference management tool for scientists
University of Kassel

http://www.zotero.org/
Free online reference management tool for scientists
WordPress

http://www.2collab.com/
Free online group collaboration tool for scientists
Elsevier B.V.


Otherwaise, for Desktop solutions see a comparision:


Reference Management Software Comparison:
http://en.wikipedia.org/wiki/Comparison_of_reference_management_software
http://mahbub.wordpress.com/2007/03/04/comparison-of-free-bibliographic-managers/

Dietrich 


--
Mr. Dietrich Rordorf
MDPI Center
Matthaeusstrasse 11
CH-4057 Basel
Switzerland

E-mail: [EMAIL PROTECTED]
Skype:  d.rordorf

Tel. +41 61 683 77 34 (office)
Tel. +41 76 561 41 83 (mobile)
Fax  +41 61 302 89 18 

 



 

 Subject:
 Re: [NTG-context] Bibliographic Databases
 From:
 Robin Kirkham [EMAIL PROTECTED]
 Date:
 Sun, 20 Apr 2008 19:13:28 +1000
 To:
 ntg-context@ntg.nl

 To:
 ntg-context@ntg.nl


 On 20 April 2008, George N. White III [EMAIL PROTECTED] wrote:

 On Thu, Apr 17, 2008 at 11:19 AM, Robin Kirkham 
 [EMAIL PROTECTED] wrote:

  I want to set up a shared bibliographic reference database for my
  research group, [...]

 I can tell you a few things that don't work!  In our lab we have both
 TeX and Word users.  Many of them had been using a DOS package
 called papyrus, using a special markup that could be translated
 to tex (.bbl) files.  Nothing we found was really satisfactory, so
 we bought EndNote, which could import from papyrus via refer
 format and can export to almost bibtex.  One problem is that
 EndNote uses unicode, so we end up with è, etc. that must
 be translated for some user's versions of bibtex.  The database
 now has a nearly infinite variety of different quote marks:
 `a`, 'a', ``a'', a, etc. depending on how the entry was made
 (many are pasted from online or pdf sources).

 EndNote is really designed for individual users, although sold
 in bulk.  If 2 people open the same database on a shared
 drive they end up with a corrupt database.

 In my view, a bibliographic database needs to store each
 reference in the source or original format, whether bibtex,
 refer, or one of the newer forms, and provide translators
 and version tracking, so each file can have forks for different
 uses (e.g., ascii vs unicode char. sets) and edits can be
 preserved for the next user.  In practice, people just dump
 selected refs to a bib file, make the .bbl file, and fix problems
 there, so fixes rarely make it back to the master database.
 If they did, we would still have accents and quote marks
 being switched back and forth depending on who last used
 the entry.


 Thanks George. EndNote is I believe the corporately-approved solution 
 here, and similar disasters occur when people try and share its data 
 files. For this reason I don't call these sorts of personal-level 
 programs databases (any more than I'll call a .bib file a database).

 The TeX folk don't fare much better. Multiple personal .bib files are 
 common, often with duplicate references but different citation keys, 
 leading to rather variable results depending on who run LaTeX/ConTeXt 
 on the file. Inconsistency in data entry is also a problem, although 
 for us, accents and quotes don't seem to too big a problem. 
 (`Authorless', i.e., corporate author documents, like data sheets, 
 seems to be more of an issue).

 For this reason I'm looking for a proper SQL database solution like 
 refdb or refbase (or maybe wikindx, thanks Andreas) with a web 
 front-end that will hopefully enforce somewhat more consistent data 
 entry, and maybe even auto-generate citation keys. Taco, your remarks 
 regarding interchange formats are valuable (both refdb and refbase 
 support MODS XML output).

 Robin
 

 ___
 If your question is of interest to others as well, please add an entry to the 
 Wiki!

 maillist : ntg-context@ntg.nl / http://www.ntg.nl/mailman/listinfo/ntg-context
 webpage  : http://www.pragma-ade.nl / http://tex.aanhet.net
 archive  : https://foundry.supelec.fr/projects/contextrev/
 wiki : http://contextgarden.net
 ___
   
___
If your question is of interest to others as well, please add an entry to the 
Wiki!

maillist : ntg

Re: [NTG-context] Bibliographic Databases

2008-04-20 Thread Robin Kirkham
On 20 April 2008, George N. White III [EMAIL PROTECTED] wrote:

 On Thu, Apr 17, 2008 at 11:19 AM, Robin Kirkham  
 [EMAIL PROTECTED] wrote:

  I want to set up a shared bibliographic reference database for my
  research group, [...]

 I can tell you a few things that don't work!  In our lab we have both
 TeX and Word users.  Many of them had been using a DOS package
 called papyrus, using a special markup that could be translated
 to tex (.bbl) files.  Nothing we found was really satisfactory, so
 we bought EndNote, which could import from papyrus via refer
 format and can export to almost bibtex.  One problem is that
 EndNote uses unicode, so we end up with è, etc. that must
 be translated for some user's versions of bibtex.  The database
 now has a nearly infinite variety of different quote marks:
 `a`, 'a', ``a'', a, etc. depending on how the entry was made
 (many are pasted from online or pdf sources).

 EndNote is really designed for individual users, although sold
 in bulk.  If 2 people open the same database on a shared
 drive they end up with a corrupt database.

 In my view, a bibliographic database needs to store each
 reference in the source or original format, whether bibtex,
 refer, or one of the newer forms, and provide translators
 and version tracking, so each file can have forks for different
 uses (e.g., ascii vs unicode char. sets) and edits can be
 preserved for the next user.  In practice, people just dump
 selected refs to a bib file, make the .bbl file, and fix problems
 there, so fixes rarely make it back to the master database.
 If they did, we would still have accents and quote marks
 being switched back and forth depending on who last used
 the entry.


Thanks George. EndNote is I believe the corporately-approved solution  
here, and similar disasters occur when people try and share its data  
files. For this reason I don't call these sorts of personal-level  
programs databases (any more than I'll call a .bib file a database).

The TeX folk don't fare much better. Multiple personal .bib files are  
common, often with duplicate references but different citation keys,  
leading to rather variable results depending on who run LaTeX/ConTeXt  
on the file. Inconsistency in data entry is also a problem, although  
for us, accents and quotes don't seem to too big a problem.  
(`Authorless', i.e., corporate author documents, like data sheets,  
seems to be more of an issue).

For this reason I'm looking for a proper SQL database solution like  
refdb or refbase (or maybe wikindx, thanks Andreas) with a web front- 
end that will hopefully enforce somewhat more consistent data entry,  
and maybe even auto-generate citation keys. Taco, your remarks  
regarding interchange formats are valuable (both refdb and refbase  
support MODS XML output).

Robin
___
If your question is of interest to others as well, please add an entry to the 
Wiki!

maillist : ntg-context@ntg.nl / http://www.ntg.nl/mailman/listinfo/ntg-context
webpage  : http://www.pragma-ade.nl / http://tex.aanhet.net
archive  : https://foundry.supelec.fr/projects/contextrev/
wiki : http://contextgarden.net
___


Re: [NTG-context] Bibliographic Databases

2008-04-20 Thread Bruce D'Arcus
Taco Hoekwater taco at elvenkind.com writes:

 
 Hi,
 
 Andreas Wagner wrote:
  Just out of curiosity: What are your reasons for preferring this over TEI:
 
 MODS was a logical choice mostly my background (scientific publishers
 = MARC databases = MODS), and that BruceD'Arcus liked it.  Btw,
 his blog is full of bibliographic articles, if you are interested:
 
http://community.muohio.edu/blogs/darcusb/
 
 (but it looks like he has switched over to RDF now)

Yes, but ...
 
 I am not really set to any particular xml format, and there are
 more mainstream choices (risx comes to mind).

... I'd say for the design of something like mbib v2 I'd advocate an internal
model that abstracts away from any particular more concrete representation. So
think in terms of maybe a standard input driver, but leave room for easy
development of others. 

There's some work going on a Python version of my citeproc effort, for example,
and he's planning input drivers for MODS, RDF, BibTeX, etc.

http://xbiblio.svn.sourceforge.net/viewvc/xbiblio/citeproc-py/citeproc/

This makes is easy for someone to write another input driver for some SQL model.
 
 But the few times I've had to work with TEI stuff I found that you
 can easily get much more than you bargained for. Bibliographic data
 is not easy on its own, and a format that allows (almost promotes)
 extra tags to be embedded also is not helping at all.
 
 Look at this:
 
http://www.tei-c.org/release/doc/tei-p5-doc/html/ref-author.html
 
 Just the 'core' module is already pretty complex, but 'namesdates'
 and 'linking' are definately also required for a useful bibliographic
 database.
 
 The nice, consise examples in the TEI docs are misleading because
 
authorLucy Allen Paton/author
 
 is useless, more specifics are needed. We need at least this:
 
author
  persName
forenameLucy/forename
forenameAllen/forename
surnamePaton/surname
  /persName
/author
 
 But with the use of persName, there are suddenly a gazillion
 ways an author can encode the same name  (and it does not
 preclude any of the other ways to encode a name).
 
http://www.tei-c.org/release/doc/tei-p5-doc/html/ND.html#NDPER
 
 Etc. etc. Imagine having to support that in a simple context module.

In the XML citation style language I designed [1] (which *could* serve as the
basis for that internal model I mention above), there's an implicit notion
that any name can have both a sort form and a display form, and that they may
(but in contexts like Eastern Europe or Asia often don't) differ. 

This makes things in many ways both simpler, and more general (works for
organizations, as well as is more international-friendly than traditional
first/last). You just handle the details you note above in the input drive code.

Bruce

[1]
http://xbiblio.svn.sourceforge.net/viewvc/xbiblio/csl/schema/trunk/csl.rnc?view=markup

___
If your question is of interest to others as well, please add an entry to the 
Wiki!

maillist : ntg-context@ntg.nl / http://www.ntg.nl/mailman/listinfo/ntg-context
webpage  : http://www.pragma-ade.nl / http://tex.aanhet.net
archive  : https://foundry.supelec.fr/projects/contextrev/
wiki : http://contextgarden.net
___


Re: [NTG-context] Bibliographic Databases

2008-04-20 Thread Bruce D\'Arcus
Taco Hoekwater taco at elvenkind.com writes:

[snip]

 But the few times I've had to work with TEI stuff I found that you
 can easily get much more than you bargained for. Bibliographic data
 is not easy on its own, and a format that allows (almost promotes)
 extra tags to be embedded also is not helping at all.

... MODS has some of these issues too. Consider these are both valid:

name type=personal
  namePartJane Doe/namePart
  role
roleTerm type=textcreator/roleTerm
  /role
/name

name type=personal
  namePart type=givenJane/namePart
  namePart type=familyDoe/namePart
  role
roleTerm type=textcreator/roleTerm
  /role
/name

So in many formats there's a balance between flexibility and
brevity/predictability. 

FWIW, I've just settled on RDF for my own data needs between it provides the
formal rigor of relational databases (that XML per se lacks), but much more
flexibility. 

But as I said in the previous note, I don't think the data format has to matter
that much to formatting software (at its core that is).

Bruce

___
If your question is of interest to others as well, please add an entry to the 
Wiki!

maillist : ntg-context@ntg.nl / http://www.ntg.nl/mailman/listinfo/ntg-context
webpage  : http://www.pragma-ade.nl / http://tex.aanhet.net
archive  : https://foundry.supelec.fr/projects/contextrev/
wiki : http://contextgarden.net
___


Re: [NTG-context] Bibliographic Databases

2008-04-19 Thread George N. White III
On Thu, Apr 17, 2008 at 11:19 AM, Robin Kirkham [EMAIL PROTECTED] wrote:

 Dear all,

  I want to set up a shared bibliographic reference database for my
  research group, and I'm looking at software like refbase http://
  refbase.sourceforge.net/ or refdb http://refdb.sourceforge.net/ to
  replace the somewhat random collection of personal BibTeX .bib files
  we have.

  Does anyone have any experience or advice to offer in using such
  things, and hooking them up to ConTeXt?  Most of these systems will
  of course emit a .bib file which will obviously work, but will any
  emit the .bbl so I can forget about BibTeX?  Will luatex one day
  connect to a bib database and fetch the details of a cited
  reference?  Is there a ConTeXt approved way forward for this sort
  of thing?

I can tell you a few things that don't work!  In our lab we have both
TeX and Word users.  Many of them had been using a DOS package
called papyrus, using a special markup that could be translated
to tex (.bbl) files.  Nothing we found was really satisfactory, so
we bought EndNote, which could import from papyrus via refer
format and can export to almost bibtex.  One problem is that
EndNote uses unicode, so we end up with è, etc. that must
be translated for some user's versions of bibtex.  The database
now has a nearly infinite variety of different quote marks:
`a`, 'a', ``a'', a, etc. depending on how the entry was made
(many are pasted from online or pdf sources).

EndNote is really designed for individual users, although sold
in bulk.  If 2 people open the same database on a shared
drive they end up with a corrupt database.

In my view, a bibliographic database needs to store each
reference in the source or original format, whether bibtex,
refer, or one of the newer forms, and provide translators
and version tracking, so each file can have forks for different
uses (e.g., ascii vs unicode char. sets) and edits can be
preserved for the next user.  In practice, people just dump
selected refs to a bib file, make the .bbl file, and fix problems
there, so fixes rarely make it back to the master database.
If they did, we would still have accents and quote marks
being switched back and forth depending on who last used
the entry.


-- 
George N. White III [EMAIL PROTECTED]
Head of St. Margarets Bay, Nova Scotia
___
If your question is of interest to others as well, please add an entry to the 
Wiki!

maillist : ntg-context@ntg.nl / http://www.ntg.nl/mailman/listinfo/ntg-context
webpage  : http://www.pragma-ade.nl / http://tex.aanhet.net
archive  : https://foundry.supelec.fr/projects/contextrev/
wiki : http://contextgarden.net
___


Re: [NTG-context] Bibliographic Databases

2008-04-18 Thread Taco Hoekwater


Robin Kirkham wrote:
 Does anyone have any experience or advice to offer in using such  
 things, and hooking them up to ConTeXt?  Most of these systems will  
 of course emit a .bib file which will obviously work, but will any  

Please have a look at the biblographic module. It comes with its own
bst files that convert bib to a private data format.

   http://modules.contextgarden.net/bib

Currently, the bibliographic module only supports .bib files, but:
if you want to be ready for the future, find a reference manager
that can export to MODS:

   http://www.loc.gov/standards/mods/

Best wishes,
Taco
___
If your question is of interest to others as well, please add an entry to the 
Wiki!

maillist : ntg-context@ntg.nl / http://www.ntg.nl/mailman/listinfo/ntg-context
webpage  : http://www.pragma-ade.nl / http://tex.aanhet.net
archive  : https://foundry.supelec.fr/projects/contextrev/
wiki : http://contextgarden.net
___


Re: [NTG-context] Bibliographic Databases

2008-04-18 Thread Wolfgang Schuster
On Fri, Apr 18, 2008 at 10:08 AM, Taco Hoekwater [EMAIL PROTECTED] wrote:


 Robin Kirkham wrote:
  Does anyone have any experience or advice to offer in using such
  things, and hooking them up to ConTeXt?  Most of these systems will
  of course emit a .bib file which will obviously work, but will any

 Please have a look at the biblographic module. It comes with its own
 bst files that convert bib to a private data format.

   http://modules.contextgarden.net/bib

 Currently, the bibliographic module only supports .bib files, but:
 if you want to be ready for the future, find a reference manager
 that can export to MODS:

   http://www.loc.gov/standards/mods/

Or even better write a new bib module with xml in MODS format as database :-)

Wolfgang
___
If your question is of interest to others as well, please add an entry to the 
Wiki!

maillist : ntg-context@ntg.nl / http://www.ntg.nl/mailman/listinfo/ntg-context
webpage  : http://www.pragma-ade.nl / http://tex.aanhet.net
archive  : https://foundry.supelec.fr/projects/contextrev/
wiki : http://contextgarden.net
___


Re: [NTG-context] Bibliographic Databases

2008-04-18 Thread Andreas Wagner
Hello Taco, hello list,

* Taco Hoekwater wrote on Apr/18/2008:
 if you want to be ready for the future, find a reference manager that can 
 export to MODS:

   http://www.loc.gov/standards/mods/

Just out of curiosity: What are your reasons for preferring this over TEI:

http://www.tei-c.org/release/doc/tei-p5-doc/html/CO.html#COBI

(I have only by your mail learnt about MODS and am currently working through 
it, so please excuse me if that 
question doesn't even make sense at all.)

Thanks,
Andreas
___
If your question is of interest to others as well, please add an entry to the 
Wiki!

maillist : ntg-context@ntg.nl / http://www.ntg.nl/mailman/listinfo/ntg-context
webpage  : http://www.pragma-ade.nl / http://tex.aanhet.net
archive  : https://foundry.supelec.fr/projects/contextrev/
wiki : http://contextgarden.net
___


Re: [NTG-context] Bibliographic Databases

2008-04-18 Thread Taco Hoekwater
Hi,

Andreas Wagner wrote:
 Just out of curiosity: What are your reasons for preferring this over TEI:

MODS was a logical choice mostly my background (scientific publishers
= MARC databases = MODS), and that BruceD'Arcus liked it.  Btw,
his blog is full of bibliographic articles, if you are interested:

   http://community.muohio.edu/blogs/darcusb/

(but it looks like he has switched over to RDF now)

I am not really set to any particular xml format, and there are
more mainstream choices (risx comes to mind).

But the few times I've had to work with TEI stuff I found that you
can easily get much more than you bargained for. Bibliographic data
is not easy on its own, and a format that allows (almost promotes)
extra tags to be embedded also is not helping at all.

Look at this:

   http://www.tei-c.org/release/doc/tei-p5-doc/html/ref-author.html

Just the 'core' module is already pretty complex, but 'namesdates'
and 'linking' are definately also required for a useful bibliographic
database.

The nice, consise examples in the TEI docs are misleading because

   authorLucy Allen Paton/author

is useless, more specifics are needed. We need at least this:

   author
 persName
   forenameLucy/forename
   forenameAllen/forename
   surnamePaton/surname
 /persName
   /author

But with the use of persName, there are suddenly a gazillion
ways an author can encode the same name  (and it does not
preclude any of the other ways to encode a name).

   http://www.tei-c.org/release/doc/tei-p5-doc/html/ND.html#NDPER

Etc. etc. Imagine having to support that in a simple context module.

Cheers, Taco


___
If your question is of interest to others as well, please add an entry to the 
Wiki!

maillist : ntg-context@ntg.nl / http://www.ntg.nl/mailman/listinfo/ntg-context
webpage  : http://www.pragma-ade.nl / http://tex.aanhet.net
archive  : https://foundry.supelec.fr/projects/contextrev/
wiki : http://contextgarden.net
___


[NTG-context] Bibliographic Databases

2008-04-17 Thread Robin Kirkham
Dear all,

I want to set up a shared bibliographic reference database for my  
research group, and I'm looking at software like refbase http:// 
refbase.sourceforge.net/ or refdb http://refdb.sourceforge.net/ to  
replace the somewhat random collection of personal BibTeX .bib files  
we have.

Does anyone have any experience or advice to offer in using such  
things, and hooking them up to ConTeXt?  Most of these systems will  
of course emit a .bib file which will obviously work, but will any  
emit the .bbl so I can forget about BibTeX?  Will luatex one day  
connect to a bib database and fetch the details of a cited  
reference?  Is there a ConTeXt approved way forward for this sort  
of thing?

Thanks in advance, Robin
___
If your question is of interest to others as well, please add an entry to the 
Wiki!

maillist : ntg-context@ntg.nl / http://www.ntg.nl/mailman/listinfo/ntg-context
webpage  : http://www.pragma-ade.nl / http://tex.aanhet.net
archive  : https://foundry.supelec.fr/projects/contextrev/
wiki : http://contextgarden.net
___


Re: [NTG-context] Bibliographic Databases

2008-04-17 Thread Andreas Wagner
Hello Robin, hello list,

* Robin Kirkham wrote on Apr/18/2008:
 I want to set up a shared bibliographic reference database for my  research 
 group, and I'm looking at 
 software like refbase http://refbase.sourceforge.net/ or refdb 
 http://refdb.sourceforge.net/ to  replace 
 the somewhat random collection of personal BibTeX .bib files  we have.

 Does anyone have any experience or advice to offer in using such  things, and 
 hooking them up to ConTeXt?  
 Most of these systems will  of course emit a .bib file which will obviously 
 work, but will any  emit the 
 .bbl so I can forget about BibTeX?  Will luatex one day  connect to a bib 
 database and fetch the details 
 of a cited  reference?  Is there a ConTeXt approved way forward for this 
 sort  of thing?

Not that I am able to help you very much further, but I am right now in a 
similar situation. I am in the 
process of setting up a db with wikindx http://wikindx.sf.net/ The main 
developer is obviously not working 
with any TeX flavour, but there is some Bibtex im-/export (which also concerns 
only .bib files) that I am 
ATM fiddling with, but I thought I might add that one to the list of databases 
you mentioned.

Cheers,
Andreas
___
If your question is of interest to others as well, please add an entry to the 
Wiki!

maillist : ntg-context@ntg.nl / http://www.ntg.nl/mailman/listinfo/ntg-context
webpage  : http://www.pragma-ade.nl / http://tex.aanhet.net
archive  : https://foundry.supelec.fr/projects/contextrev/
wiki : http://contextgarden.net
___