[Bibdesk-users] request for feature (was Re: BibDesk to Connotea to BibDesk)

2007-10-09 Thread P Kishor
Follow-up...

would it be possible to have a field in which one could enter a PMID,
ASIN, DOI, or ISBN, and have all the relevant fields filled magically?

Librarything seems to have something like this, but only for ISBN/books.

On 10/9/07, P Kishor [EMAIL PROTECTED] wrote:
 In my quest to put up my citations in a place where they can be shared
 with others, I started exploring Connotea (http://www.connotea.org),
 an open source online citations manager created by Nature.com and let
 loose in the wild.

 Well, I started by importing my BibDesk bib into Connotea. After
 whirring for about 20 mins, it reported that out of my 98 citations,
 only 40 had been imported. The primary cause of not importing the bulk
 of the remaining 58 was missing URI, PMID, ASIN, or DOI. A quick
 Google-ing explained to me what the heck that meant, and indeed, I
 didn't have a PubMed Unique Identifier, an Amazon Standard
 Identification Number, or a Digital Object Identifier let alone a
 URI from which Connotea could have retrieved the requisite info.

 I am thankful for BibDesk being lenient and not rejecting my entries,
 but now I am thinking -- what is it that I can do to make my
 bibliography more complete, accurate, and reliable.

 I realize this is not a BibDesk-specific question, but most of you
 know way more than I do about citations and bibliographies, so I
 hope you can teach me a few things here. Eventually I want my entire
 BibDesk to be imported into Connotea (or any other such site that you
 might suggest as being better) and back again, if required.

 Many thanks in advance.




-- 
Puneet Kishor
http://punkish.eidesis.org/
Nelson Institute for Environmental Studies
http://www.nelson.wisc.edu/
Open Source Geospatial Foundation (OSGeo)
http://www.osgeo.org/
Summer 2007 ST Policy Fellow, The National Academies
http://www.nas.edu/

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Re: [Bibdesk-users] request for feature (was Re: BibDesk to Connotea to BibDesk)

2007-10-09 Thread François Briatte
When I import from PubMed using the BibDesk command, the PMID field is
added appropriately (same as the DOI if memory serves). I have no
knowledge of an Import from Amazon function.

Why not use citeulike instead? It seems more flexible and more
evolutive. Here's an old idea of workflow I had about BibDesk and
CiteULike: http://phnk.com/blog/tech/citeulike-and-bibdesk/

Fr.

On 09/10/2007, P Kishor [EMAIL PROTECTED] wrote:
 Follow-up...

 would it be possible to have a field in which one could enter a PMID,
 ASIN, DOI, or ISBN, and have all the relevant fields filled magically?

 Librarything seems to have something like this, but only for ISBN/books.

 On 10/9/07, P Kishor [EMAIL PROTECTED] wrote:
  In my quest to put up my citations in a place where they can be shared
  with others, I started exploring Connotea (http://www.connotea.org),
  an open source online citations manager created by Nature.com and let
  loose in the wild.
 
  Well, I started by importing my BibDesk bib into Connotea. After
  whirring for about 20 mins, it reported that out of my 98 citations,
  only 40 had been imported. The primary cause of not importing the bulk
  of the remaining 58 was missing URI, PMID, ASIN, or DOI. A quick
  Google-ing explained to me what the heck that meant, and indeed, I
  didn't have a PubMed Unique Identifier, an Amazon Standard
  Identification Number, or a Digital Object Identifier let alone a
  URI from which Connotea could have retrieved the requisite info.
 
  I am thankful for BibDesk being lenient and not rejecting my entries,
  but now I am thinking -- what is it that I can do to make my
  bibliography more complete, accurate, and reliable.
 
  I realize this is not a BibDesk-specific question, but most of you
  know way more than I do about citations and bibliographies, so I
  hope you can teach me a few things here. Eventually I want my entire
  BibDesk to be imported into Connotea (or any other such site that you
  might suggest as being better) and back again, if required.
 
  Many thanks in advance.
 



 --
 Puneet Kishor
 http://punkish.eidesis.org/
 Nelson Institute for Environmental Studies
 http://www.nelson.wisc.edu/
 Open Source Geospatial Foundation (OSGeo)
 http://www.osgeo.org/
 Summer 2007 ST Policy Fellow, The National Academies
 http://www.nas.edu/

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 Now Search log events and configuration files using AJAX and a browser.
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 https://lists.sourceforge.net/lists/listinfo/bibdesk-users


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Re: [Bibdesk-users] request for feature (was Re: BibDesk to Connotea to BibDesk)

2007-10-09 Thread P Kishor
Thanks for the advice. I am now trying citeulike as suggested, but not
very successful at this as well. I am getting a lot of errors like so,
and then nothing is imported --

Didn't quite work..

I got this error when I tried to parse your file
This is BibTeX, Version 0.99c (Web2C 7.5.4)
The top-level auxiliary file: /tmp/fileEQXFEZ.aux
The style file: citeulike.bst
Database file #1: fileEQXFEZ.bib
Warning--entry type for Manso:2007aa isn't style-file defined
--line 149 of file fileEQXFEZ.bib
Warning--entry type for Stiglitz:2005aa isn't style-file defined
--line 272 of file fileEQXFEZ.bib
Your field is more than 5000 characters---line 433 of file fileEQXFEZ.bib
 : The great irony is that the U.S. economy in its early years was
built in large part on a lax attitude toward intellectual-property
rights and enforcement. As the historian Doron Ben-Atar shows in his
book Trade Secrets, the Founders believed that a strict attitude
toward patents and copyright would limit dom
 :



  estic innovation and make it harder
for the U.S. to expand its industrial base. American law did not
protect the rights of foreign inventors or writers, and Secretary of
the Treasury Alexander Hamilton, in his famous Report on
Manufactures, of 1791, actively advocated the theft of technology and
the luring of skilled workers from foreign countries. Among the
beneficiaries of this was the American textile industry, which
flourished thanks to pirated technology. Free-trade agreements that
export our own restrictive I.P. laws may make the world safe for
Pfizer, Microsoft, and Disney, but they don't deserve the name free
trade.},
I'm skipping whatever remains of this entry
Your field is more than 5000 characters---line 550 of file fileEQXFEZ.bib
 : I have no problem with an individual who faces unusual threats
from publication of her identity or identifying details being able
under the law to seek special exception from openness, said Rebecca
Daugherty, the director of the Freedo
 :


   m of Information Service Center for the
Reporters Committee for Freedom of the Press in Virginia. But the
secrecy should be the exception, she said, not the rule.
I'm skipping whatever remains of this entry
Your field is more than 5000 characters---line 727 of file fileEQXFEZ.bib
 : policies far exceed any revenues that might be generated through co
 :
st recovery policies;
I'm skipping whatever remains of this entry
Your field is more than 5000 characters---line 899 of file fileEQXFEZ.bib
 : data and analyzed several different potential legislative models
for database prote
 :
   ction in the United States from
I'm skipping whatever remains of this entry
Warning--entry type for Harkins:aa isn't style-file defined
--line 999 of file fileEQXFEZ.bib
Warning--entry type for Shapiro:aa isn't style-file defined
--line 1007 of file fileEQXFEZ.bib
Warning--entry type for Pareles:aa isn't style-file defined
--line 1037 of file fileEQXFEZ.bib
Warning--entry type for Friedman:aa isn't style-file defined
--line 1056 of file fileEQXFEZ.bib
Warning--entry type for Bonaccorsi:aa isn't style-file defined
--line 1065 of file fileEQXFEZ.bib
Warning--entry type for Schroer:2007aa isn't style-file defined
--line 1084 of file fileEQXFEZ.bib
Warning--entry type for Friedman:2007aa isn't style-file defined
--line 1122 of file fileEQXFEZ.bib
Warning--entry type for Raymond:2000aa isn't style-file defined
--line 1145 of file fileEQXFEZ.bib
Warning--entry type for Coase:aa isn't style-file defined
--line 1155 of file fileEQXFEZ.bib
Warning--entry type for Torkington:aa isn't style-file defined
--line 1198 of file fileEQXFEZ.bib
Warning--entry type for Jobs:2007aa isn't style-file defined
--line 1241 of file fileEQXFEZ.bib
Warning--entry type for Wheeler:aa isn't style-file defined
--line 1342 of file fileEQXFEZ.bib
Warning--entry type for Rifkin:aa isn't style-file defined
--line 1419 of file fileEQXFEZ.bib
Your field is more than 5000 characters---line 1498 of file fileEQXFEZ.bib
 : [One of the marks of a great class is, in m
 :y view, identifying at
least one view-changing text. In the last edition of this class last
semester, for me, it was Schumpeter's Creative Destruction. This
time around, it is not Thornton directly, but a work that Thornton
rerferences with great and justified reverence -- Max Weber's 1904
treatise on Die protestantische Ethik und der 'Geist' des
Kapitalismus or The Protestant Ethic and the Spirit of Capitalism.
I got the book today and feel a bit defeated by its density, but do
intend to slog through it to the extent I can. Hopefully he writes as
well as our friend Schumpeter.]},
I'm skipping whatever remains of this entry
Your field is more than 5000 characters---line 1555 of file fileEQXFEZ.bib
 :  My first thoughts concerning this paper are related the fact that
this is among the first social science papers that I have ever read.
I was 

Re: [Bibdesk-users] request for feature (was Re: BibDesk to Connotea to BibDesk)

2007-10-09 Thread François Briatte
Sorry, what do you mean by 'my' file?

Also, warnings are normal, especially if you forget to mention the
authors or use unconventional types.

On 09/10/2007, P Kishor [EMAIL PROTECTED] wrote:
 Thanks for the advice. I am now trying citeulike as suggested, but not
 very successful at this as well. I am getting a lot of errors like so,
 and then nothing is imported --

 Didn't quite work..

 I got this error when I tried to parse your file
 This is BibTeX, Version 0.99c (Web2C 7.5.4)
 The top-level auxiliary file: /tmp/fileEQXFEZ.aux
 The style file: citeulike.bst
 Database file #1: fileEQXFEZ.bib
 Warning--entry type for Manso:2007aa isn't style-file defined
 --line 149 of file fileEQXFEZ.bib
 Warning--entry type for Stiglitz:2005aa isn't style-file defined
 --line 272 of file fileEQXFEZ.bib
 Your field is more than 5000 characters---line 433 of file fileEQXFEZ.bib
  : The great irony is that the U.S. economy in its early years was
 built in large part on a lax attitude toward intellectual-property
 rights and enforcement. As the historian Doron Ben-Atar shows in his
 book Trade Secrets, the Founders believed that a strict attitude
 toward patents and copyright would limit dom
  :



   estic innovation and make it harder
 for the U.S. to expand its industrial base. American law did not
 protect the rights of foreign inventors or writers, and Secretary of
 the Treasury Alexander Hamilton, in his famous Report on
 Manufactures, of 1791, actively advocated the theft of technology and
 the luring of skilled workers from foreign countries. Among the
 beneficiaries of this was the American textile industry, which
 flourished thanks to pirated technology. Free-trade agreements that
 export our own restrictive I.P. laws may make the world safe for
 Pfizer, Microsoft, and Disney, but they don't deserve the name free
 trade.},
 I'm skipping whatever remains of this entry
 Your field is more than 5000 characters---line 550 of file fileEQXFEZ.bib
  : I have no problem with an individual who faces unusual threats
 from publication of her identity or identifying details being able
 under the law to seek special exception from openness, said Rebecca
 Daugherty, the director of the Freedo
  :


m of Information Service Center for the
 Reporters Committee for Freedom of the Press in Virginia. But the
 secrecy should be the exception, she said, not the rule.
 I'm skipping whatever remains of this entry
 Your field is more than 5000 characters---line 727 of file fileEQXFEZ.bib
  : policies far exceed any revenues that might be generated through co
  :
 st recovery policies;
 I'm skipping whatever remains of this entry
 Your field is more than 5000 characters---line 899 of file fileEQXFEZ.bib
  : data and analyzed several different potential legislative models
 for database prote
  :
ction in the United States from
 I'm skipping whatever remains of this entry
 Warning--entry type for Harkins:aa isn't style-file defined
 --line 999 of file fileEQXFEZ.bib
 Warning--entry type for Shapiro:aa isn't style-file defined
 --line 1007 of file fileEQXFEZ.bib
 Warning--entry type for Pareles:aa isn't style-file defined
 --line 1037 of file fileEQXFEZ.bib
 Warning--entry type for Friedman:aa isn't style-file defined
 --line 1056 of file fileEQXFEZ.bib
 Warning--entry type for Bonaccorsi:aa isn't style-file defined
 --line 1065 of file fileEQXFEZ.bib
 Warning--entry type for Schroer:2007aa isn't style-file defined
 --line 1084 of file fileEQXFEZ.bib
 Warning--entry type for Friedman:2007aa isn't style-file defined
 --line 1122 of file fileEQXFEZ.bib
 Warning--entry type for Raymond:2000aa isn't style-file defined
 --line 1145 of file fileEQXFEZ.bib
 Warning--entry type for Coase:aa isn't style-file defined
 --line 1155 of file fileEQXFEZ.bib
 Warning--entry type for Torkington:aa isn't style-file defined
 --line 1198 of file fileEQXFEZ.bib
 Warning--entry type for Jobs:2007aa isn't style-file defined
 --line 1241 of file fileEQXFEZ.bib
 Warning--entry type for Wheeler:aa isn't style-file defined
 --line 1342 of file fileEQXFEZ.bib
 Warning--entry type for Rifkin:aa isn't style-file defined
 --line 1419 of file fileEQXFEZ.bib
 Your field is more than 5000 characters---line 1498 of file fileEQXFEZ.bib
  : [One of the marks of a great class is, in m
  :y view, identifying at
 least one view-changing text. In the last edition of this class last
 semester, for me, it was Schumpeter's Creative Destruction. This
 time around, it is not Thornton directly, but a work that Thornton
 rerferences with great and justified reverence -- Max Weber's 1904
 treatise on Die protestantische Ethik und der 'Geist' des
 Kapitalismus or The Protestant Ethic and the Spirit of Capitalism.
 I got the book today and feel a bit defeated by its density, but do
 intend to slog through it to the extent I can. Hopefully he writes as
 well as our 

Re: [Bibdesk-users] request for feature (was Re: BibDesk to Connotea to BibDesk)

2007-10-09 Thread Michael McCracken
On 10/9/07, François Briatte [EMAIL PROTECTED] wrote:
 When I import from PubMed using the BibDesk command, the PMID field is
 added appropriately (same as the DOI if memory serves). I have no
 knowledge of an Import from Amazon function.

 Why not use citeulike instead? It seems more flexible and more
 evolutive. Here's an old idea of workflow I had about BibDesk and
 CiteULike: http://phnk.com/blog/tech/citeulike-and-bibdesk/

François, you might be interested in recent changes to the 'web group'
functionality.
We have added an easier method of importing items into BibDesk from
citeulike, which is an extension of the feature I wrote about here:
http://michael-mccracken.net/wp/2007/01/26/bibdesk-and-the-hcite-microformat/

It is available in current nightly builds, if you are feeling adventurous. :)

-mike

 Fr.

 On 09/10/2007, P Kishor [EMAIL PROTECTED] wrote:
  Follow-up...
 
  would it be possible to have a field in which one could enter a PMID,
  ASIN, DOI, or ISBN, and have all the relevant fields filled magically?
 
  Librarything seems to have something like this, but only for ISBN/books.
 
  On 10/9/07, P Kishor [EMAIL PROTECTED] wrote:
   In my quest to put up my citations in a place where they can be shared
   with others, I started exploring Connotea (http://www.connotea.org),
   an open source online citations manager created by Nature.com and let
   loose in the wild.
  
   Well, I started by importing my BibDesk bib into Connotea. After
   whirring for about 20 mins, it reported that out of my 98 citations,
   only 40 had been imported. The primary cause of not importing the bulk
   of the remaining 58 was missing URI, PMID, ASIN, or DOI. A quick
   Google-ing explained to me what the heck that meant, and indeed, I
   didn't have a PubMed Unique Identifier, an Amazon Standard
   Identification Number, or a Digital Object Identifier let alone a
   URI from which Connotea could have retrieved the requisite info.
  
   I am thankful for BibDesk being lenient and not rejecting my entries,
   but now I am thinking -- what is it that I can do to make my
   bibliography more complete, accurate, and reliable.
  
   I realize this is not a BibDesk-specific question, but most of you
   know way more than I do about citations and bibliographies, so I
   hope you can teach me a few things here. Eventually I want my entire
   BibDesk to be imported into Connotea (or any other such site that you
   might suggest as being better) and back again, if required.
  
   Many thanks in advance.
  
 
 
 
  --
  Puneet Kishor
  http://punkish.eidesis.org/
  Nelson Institute for Environmental Studies
  http://www.nelson.wisc.edu/
  Open Source Geospatial Foundation (OSGeo)
  http://www.osgeo.org/
  Summer 2007 ST Policy Fellow, The National Academies
  http://www.nas.edu/
 
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  https://lists.sourceforge.net/lists/listinfo/bibdesk-users
 

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-- 
Michael McCracken
UCSD CSE PhD Candidate
research: http://www.cse.ucsd.edu/~mmccrack/
misc: http://michael-mccracken.net/wp/

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Re: [Bibdesk-users] request for feature (was Re: BibDesk to Connotea to BibDesk)

2007-10-09 Thread jiho

On 2007-October-09  , at 22:02 , P Kishor wrote:
 On 10/9/07, François Briatte [EMAIL PROTECTED] wrote:
 Sorry, what do you mean by 'my' file?

 I am not sure what you mean by that question. I am looking at my
 response and I don't see any reference to my file. I said
 specifically (quoting myself) --

The error message from CiteULike starts by:
I got this error when I tried to parse your file
In this case your file is the file from P Kishor he is trying to  
import.

 Thanks for the advice. I am now trying citeulike as suggested,  
 but not
 very successful at this as well. I am getting a lot of errors  
 like so,
 and then nothing is imported --

 everything else is errors reported by CituULike.

 Also, warnings are normal, especially if you forget to mention the
 authors or use unconventional types.

 Yes, I would think so, no? Except, nothing gets imported. My CituULike
 library is empty. Seems like I am using unconventional types except
 I am not quite sure what convention to apply to the ones that are
 erroneous as reported by CiteULike. Besides, as you yourself said,
 CiteULike should import at least the others (I have around 100
 entries, and less than 20 show up in the CiteULike's import error
 log). But, nothing is imported.

I suspect it to be caused by your citekey format. I am not sure CuL  
can deal with the colon ( : ) in the citekey. Given the error message  
(lots of colons inside) I guess CuL breaks citekeys at colons and  
trys to read the rest as a field, until the next colon. Try with  
another citekey format. The colons there are not very safe anyway.

JiHO
---
http://jo.irisson.free.fr/



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Re: [Bibdesk-users] request for feature (was Re: BibDesk to Connotea to BibDesk)

2007-10-09 Thread P Kishor
On 10/9/07, jiho [EMAIL PROTECTED] wrote:

 On 2007-October-09  , at 22:02 , P Kishor wrote:
  On 10/9/07, François Briatte [EMAIL PROTECTED] wrote:
  Sorry, what do you mean by 'my' file?
 
  I am not sure what you mean by that question. I am looking at my
  response and I don't see any reference to my file. I said
  specifically (quoting myself) --

 The error message from CiteULike starts by:
 I got this error when I tried to parse your file
 In this case your file is the file from P Kishor he is trying to
 import.

  Thanks for the advice. I am now trying citeulike as suggested,
  but not
  very successful at this as well. I am getting a lot of errors
  like so,
  and then nothing is imported --
 
  everything else is errors reported by CituULike.
 
  Also, warnings are normal, especially if you forget to mention the
  authors or use unconventional types.
 
  Yes, I would think so, no? Except, nothing gets imported. My CituULike
  library is empty. Seems like I am using unconventional types except
  I am not quite sure what convention to apply to the ones that are
  erroneous as reported by CiteULike. Besides, as you yourself said,
  CiteULike should import at least the others (I have around 100
  entries, and less than 20 show up in the CiteULike's import error
  log). But, nothing is imported.

 I suspect it to be caused by your citekey format. I am not sure CuL
 can deal with the colon ( : ) in the citekey. Given the error message
 (lots of colons inside) I guess CuL breaks citekeys at colons and
 trys to read the rest as a field, until the next colon. Try with
 another citekey format. The colons there are not very safe anyway.



yikes! Thanks for the tip... will try it. I didn't make up that
citekey format... that is what I got from BibDesk out of the box.
Anyway, will tinker with that and hopefully will be able to report
success.


-- 
Puneet Kishor
http://punkish.eidesis.org/
Nelson Institute for Environmental Studies
http://www.nelson.wisc.edu/
Open Source Geospatial Foundation (OSGeo)
http://www.osgeo.org/
Summer 2007 ST Policy Fellow, The National Academies
http://www.nas.edu/

-
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Still grepping through log files to find problems?  Stop.
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Re: [Bibdesk-users] request for feature (was Re: BibDesk to Connotea to BibDesk)

2007-10-09 Thread P Kishor
On 10/9/07, P Kishor [EMAIL PROTECTED] wrote:
 On 10/9/07, jiho [EMAIL PROTECTED] wrote:
 
  On 2007-October-09  , at 22:02 , P Kishor wrote:
..
  
   Yes, I would think so, no? Except, nothing gets imported. My CituULike
   library is empty. Seems like I am using unconventional types except
   I am not quite sure what convention to apply to the ones that are
   erroneous as reported by CiteULike. Besides, as you yourself said,
   CiteULike should import at least the others (I have around 100
   entries, and less than 20 show up in the CiteULike's import error
   log). But, nothing is imported.
 
  I suspect it to be caused by your citekey format. I am not sure CuL
  can deal with the colon ( : ) in the citekey. Given the error message
  (lots of colons inside) I guess CuL breaks citekeys at colons and
  trys to read the rest as a field, until the next colon. Try with
  another citekey format. The colons there are not very safe anyway.
 


 yikes! Thanks for the tip... will try it. I didn't make up that
 citekey format... that is what I got from BibDesk out of the box.
 Anyway, will tinker with that and hopefully will be able to report
 success.



shucks. No luck still. Same kind of error message (see below) and then
nothing imported. How frustrating...

Didn't quite work..

I got this error when I tried to parse your file
This is BibTeX, Version 0.99c (Web2C 7.5.4)
The top-level auxiliary file: /tmp/filetqIqt0.aux
The style file: citeulike.bst
Database file #1: filetqIqt0.bib
Warning--entry type for Manso_2007_aa isn't style-file defined
--line 149 of file filetqIqt0.bib
Warning--entry type for Stiglitz__ab isn't style-file defined
--line 272 of file filetqIqt0.bib
Your field is more than 5000 characters---line 433 of file filetqIqt0.bib
 : The great irony is that the U.S. economy in its early years was
built in large part on a lax attitude toward intellectual-property
rights and enforcement. As the historian Doron Ben-Atar shows in his
book Trade Secrets, the Founders believed that a strict attitude
toward patents and copyright would limit dom
 :



  estic innovation and make it harder
for the U.S. to expand its industrial base. American law did not
protect the rights of foreign inventors or writers, and Secretary of
the Treasury Alexander Hamilton, in his famous Report on
Manufactures, of 1791, actively advocated the theft of technology and
the luring of skilled workers from foreign countries. Among the
beneficiaries of this was the American textile industry, which
flourished thanks to pirated technology. Free-trade agreements that
export our own restrictive I.P. laws may make the world safe for
Pfizer, Microsoft, and Disney, but they don't deserve the name free
trade.},
I'm skipping whatever remains of this entry
Your field is more than 5000 characters---line 550 of file filetqIqt0.bib
 : I have no problem with an individual who faces unusual threats
from publication of her identity or identifying details being able
under the law to seek special exception from openness, said Rebecca
Daugherty, the director of the Freedo
 :


   m of Information Service Center for the
Reporters Committee for Freedom of the Press in Virginia. But the
secrecy should be the exception, she said, not the rule.
I'm skipping whatever remains of this entry
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 : policies far exceed any revenues that might be generated through co
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st recovery policies;
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 : data and analyzed several different potential legislative models
for database prote
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   ction in the United States from
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