BibDesk

On May 31, 2008, at 8:39 AM, Robert Sekuler wrote:

> I use apacite.sty (and BibDesk) to prepare reference lists for
> articles, NIH progress reports and NIH grants.  As of the end of May
> 2008 NIH wants citations to include the PubMed Central ID for certain
> publications.  OK, I get that,  and when BibDesk accesses PubMed it
> downloads that PMCID number, if it's available,  as part of the bib
> info.  But apacite.sty does not output that item What is best/simplest
> way to conform to NIH's requirement?  Should I modify apacite to
> include the PMCID number in its output?  And if so, how? Or should I
> try to make a new .bst file from scratch?

Writing a new .bst file from scratch is extremely difficult, so I'd  
definitely try to modify apacite.  Make sure you copy/rename it first.

Looking at apacite.bst, I'd use the url writing code as an example, so  
you'd have something like this:

   pmcid empty$
     'skip$
     { % Clear the stack
       duplicate$ empty$
         'skip$
         { output.new.block }
       if$
       format.pmcid
     }
   if$

added to the appropriate reference types (e.g. FUNCTION  
{periodical}).  The position of this call and FUNCTION {format.pmcid}  
will depend on how NIH wants it formatted.  You'll also need to add  
pmcid to the ENTRY {} list near the top.

hth,
adam

On 31.05.2008, at 17:39, Robert Sekuler wrote:

> I use apacite.sty (and BibDesk) to prepare reference lists for
> articles, NIH progress reports and NIH grants.  As of the end of May
> 2008 NIH wants citations to include the PubMed Central ID for certain
> publications.  OK, I get that,  and when BibDesk accesses PubMed it
> downloads that PMCID number, if it's available,  as part of the bib
> info.  But apacite.sty does not output that item What is best/simplest
> way to conform to NIH's requirement?  Should I modify apacite to
> include the PMCID number in its output?  And if so, how? Or should I
> try to make a new .bst file from scratch?

Don't bother with .bst files. Have a look at the biblatex package if  
you need to come up with your own citation style. biblatex basically  
moves all bibliography formatting over to LaTeX. It's extremely  
flexible and well though out.

simon
--
Simon Spiegel
Steinhaldenstr. 50
8002 Zürich

Telephon: ++41 44 451 5334
Mobophon: ++41 76 459 60 39


http://www.simifilm.ch

„Was soll aus mir mal werden, wenn ich mal nicht mehr bin?“ Robert  
Gernhardt

On May 31, 2008, at 9:35 AM, Simon Spiegel wrote:

> On 31.05.2008, at 17:39, Robert Sekuler wrote:
>
>> I use apacite.sty (and BibDesk) to prepare reference lists for
>> articles, NIH progress reports and NIH grants.  As of the end of May
>> 2008 NIH wants citations to include the PubMed Central ID for certain
>> publications.  OK, I get that,  and when BibDesk accesses PubMed it
>> downloads that PMCID number, if it's available,  as part of the bib
>> info.  But apacite.sty does not output that item What is best/ 
>> simplest
>> way to conform to NIH's requirement?  Should I modify apacite to
>> include the PMCID number in its output?  And if so, how? Or should I
>> try to make a new .bst file from scratch?
>
> Don't bother with .bst files. Have a look at the biblatex package if
> you need to come up with your own citation style. biblatex basically
> moves all bibliography formatting over to LaTeX. It's extremely
> flexible and well though out.

Do you think that writing a style that conforms to the (very rigid)  
APA rules from scratch in biblatex is easier than modifying  
apacite.bst?  I'm a bit skeptical in this case, since no one has come  
up with an APA format for biblatex:

http://groups.google.com/group/comp.text.tex/browse_thread/thread/a2d2d8bd900ea57d

On 2008-05-31, at 9:26 AM, Adam R. Maxwell wrote:

>
> On May 31, 2008, at 8:39 AM, Robert Sekuler wrote:
>
>> I use apacite.sty (and BibDesk) to prepare reference lists for
>> articles, NIH progress reports and NIH grants.  As of the end of May
>> 2008 NIH wants citations to include the PubMed Central ID for certain
>> publications.  OK, I get that,  and when BibDesk accesses PubMed it
>> downloads that PMCID number, if it's available,  as part of the bib
>> info.  But apacite.sty does not output that item What is best/ 
>> simplest
>> way to conform to NIH's requirement?  Should I modify apacite to
>> include the PMCID number in its output?  And if so, how? Or should I
>> try to make a new .bst file from scratch?

Best/simplest way: copy the contents of pmcid to the note field for  
the publications you need.

Bibdesk doesn't have a copy field function, but you can use an  
AppleScript:

tell application "BibDesk"
	set theSelPubs to the selection of document 1
	repeat with thePub in theSelPubs
		set thePMCID to value of field "PMCID" of thePub
		set value of field "note" of thePub to thePMCID
	end repeat
end tell -- Bibdesk

Hacking the .bst would work, but this is much simpler.

-AHM

On 31.05.2008, at 18:56, Adam R. Maxwell wrote:

>
> On May 31, 2008, at 9:35 AM, Simon Spiegel wrote:
>
>> On 31.05.2008, at 17:39, Robert Sekuler wrote:
>>
>>> I use apacite.sty (and BibDesk) to prepare reference lists for
>>> articles, NIH progress reports and NIH grants.  As of the end of May
>>> 2008 NIH wants citations to include the PubMed Central ID for  
>>> certain
>>> publications.  OK, I get that,  and when BibDesk accesses PubMed it
>>> downloads that PMCID number, if it's available,  as part of the bib
>>> info.  But apacite.sty does not output that item What is best/
>>> simplest
>>> way to conform to NIH's requirement?  Should I modify apacite to
>>> include the PMCID number in its output?  And if so, how? Or should I
>>> try to make a new .bst file from scratch?
>>
>> Don't bother with .bst files. Have a look at the biblatex package if
>> you need to come up with your own citation style. biblatex basically
>> moves all bibliography formatting over to LaTeX. It's extremely
>> flexible and well though out.
>
> Do you think that writing a style that conforms to the (very rigid)
> APA rules from scratch in biblatex is easier than modifying
> apacite.bst?  I'm a bit skeptical in this case, since no one has come
> up with an APA format for biblatex:
>
> http://groups.google.com/group/comp.text.tex/browse_thread/thread/a2d2d8bd900ea57d

I don't know the APA rules, but I know  hacking .bst files and  
biblatex from my own experience both. When I tried to modify jurabib  
back then, even small changes turned into long trial and error  
sessions. With biblatex on the other hand, I was able to implement a  
quite complex style in a few days.

simon

--
Simon Spiegel
Steinhaldenstr. 50
8002 Zürich

Telephon: ++41 44 451 5334
Mobophon: ++41 76 459 60 39

http://www.simifilm.ch

„In a world getting more and more democratic, film directing is the  
last resort for dictators.“ Francis Ford Coppola

On 31.05.2008, at 19:58, Simon Spiegel wrote:

>
> On 31.05.2008, at 18:56, Adam R. Maxwell wrote:
>
>>
>> On May 31, 2008, at 9:35 AM, Simon Spiegel wrote:
>>
>>> On 31.05.2008, at 17:39, Robert Sekuler wrote:
>>>
>>>> I use apacite.sty (and BibDesk) to prepare reference lists for
>>>> articles, NIH progress reports and NIH grants.  As of the end of  
>>>> May
>>>> 2008 NIH wants citations to include the PubMed Central ID for
>>>> certain
>>>> publications.  OK, I get that,  and when BibDesk accesses PubMed it
>>>> downloads that PMCID number, if it's available,  as part of the bib
>>>> info.  But apacite.sty does not output that item What is best/
>>>> simplest
>>>> way to conform to NIH's requirement?  Should I modify apacite to
>>>> include the PMCID number in its output?  And if so, how? Or  
>>>> should I
>>>> try to make a new .bst file from scratch?
>>>
>>> Don't bother with .bst files. Have a look at the biblatex package if
>>> you need to come up with your own citation style. biblatex basically
>>> moves all bibliography formatting over to LaTeX. It's extremely
>>> flexible and well though out.
>>
>> Do you think that writing a style that conforms to the (very rigid)
>> APA rules from scratch in biblatex is easier than modifying
>> apacite.bst?  I'm a bit skeptical in this case, since no one has come
>> up with an APA format for biblatex:
>>
>> http://groups.google.com/group/comp.text.tex/browse_thread/thread/a2d2d8bd900ea57d
>
> I don't know the APA rules, but I know  hacking .bst files and
> biblatex from my own experience both. When I tried to modify jurabib
> back then, even small changes turned into long trial and error
> sessions. With biblatex on the other hand, I was able to implement a
> quite complex style in a few days.

A followup: As I said, I don't know the details of the APA style, but  
from a first glance, the examples I saw on the web don't look  
dramatically different from biblatex's authoryear-comp style. So you  
definitely wouldn't have to start from scratch but could start with an  
existing style. And even if bigger changes were necessary, contrary to  
when you hack .bst files you'd actually had a chance to understand  
what's going on.

simon
--
Simon Spiegel
Steinhaldenstr. 50
8002 Zürich

Telephon: ++41 44 451 5334
Mobophon: ++41 76 459 60 39

http://www.simifilm.ch

„I'm not that easy to impress. – O, a blue car!“ Homer Simpson