Re: [Bibdesk-users] Importing PDF files
Indeed, I would support that suggestion. I have it on since years and never regretted (so far) ;-) Regards, Andreas On 13/10/2011, at 16:32 , Gregory Jefferis wrote: > > On 12 Oct 2011, at 14:23, Adam R. Maxwell wrote: > >> >> On Oct 12, 2011, at 05:09 , M. Tamer Özsu wrote: >> >>> I was simply wondering out loud how some of these other programs manage to >>> extract the title/author/... data from the PDF files to at least attempt to >>> generate some of this citation information. I now understand that Bibdesk >>> does not do this, and that is perfectly fine. >> >> They do it by scraping information from the PDF, including the DOI. BibDesk >> can also do this, using the BDSKShouldParsePDFToGeneratePubMedSearchTerm >> hidden preference. I don't use it myself, since it only searches PubMed. >> Pretty similar code could probably be used to run a Web of Science search, >> though, come to think of it... > > Is there any reason why this is turned off by default? I actually wrote most > of that code and I thought that it had broken because I did not notice the > hidden pref. For biologists/medics, this is an incredibly timesaver and it > works with nearly all modern PDFs in this domain. > > People don't normally drop PDFs onto BibDesk unless they have an existing > reference. So I don't see that setting this to true by default would much > inconvenience anyone. Setting it to false means that very few people will > ever notice and use it. > > Best, > > Greg. > -- > All the data continuously generated in your IT infrastructure contains a > definitive record of customers, application performance, security > threats, fraudulent activity and more. Splunk takes this data and makes > sense of it. Business sense. IT sense. Common sense. > http://p.sf.net/sfu/splunk-d2d-oct > ___ > Bibdesk-users mailing list > Bibdesk-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/bibdesk-users -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2d-oct ___ Bibdesk-users mailing list Bibdesk-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/bibdesk-users
Re: [Bibdesk-users] Importing PDF files
On 12 Oct 2011, at 14:23, Adam R. Maxwell wrote: > > On Oct 12, 2011, at 05:09 , M. Tamer Özsu wrote: > >> I was simply wondering out loud how some of these other programs manage to >> extract the title/author/... data from the PDF files to at least attempt to >> generate some of this citation information. I now understand that Bibdesk >> does not do this, and that is perfectly fine. > > They do it by scraping information from the PDF, including the DOI. BibDesk > can also do this, using the BDSKShouldParsePDFToGeneratePubMedSearchTerm > hidden preference. I don't use it myself, since it only searches PubMed. > Pretty similar code could probably be used to run a Web of Science search, > though, come to think of it... Is there any reason why this is turned off by default? I actually wrote most of that code and I thought that it had broken because I did not notice the hidden pref. For biologists/medics, this is an incredibly timesaver and it works with nearly all modern PDFs in this domain. People don't normally drop PDFs onto BibDesk unless they have an existing reference. So I don't see that setting this to true by default would much inconvenience anyone. Setting it to false means that very few people will ever notice and use it. Best, Greg. -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2d-oct ___ Bibdesk-users mailing list Bibdesk-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/bibdesk-users
Re: [Bibdesk-users] Importing PDF files
On Oct 13, 2011, at 06:42 , Fischlin Andreas wrote: > I was talking only on the web scraping. That AFAIK costs a lot, e.g. > http://www.automationanywhere.com/solutions/screenScrape.htm. But perhaps > that's not an issue at all. I think we're talking at cross purposes. BibDesk's screen scraping is free; that's the technique it uses in the web group(s). The sites it can scrape, OTOH, may require a subscription for access. -- adam -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2d-oct ___ Bibdesk-users mailing list Bibdesk-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/bibdesk-users
Re: [Bibdesk-users] Importing PDF files
I was talking only on the web scraping. That AFAIK costs a lot, e.g. http://www.automationanywhere.com/solutions/screenScrape.htm. But perhaps that's not an issue at all. Regards, Andreas On 13/10/2011, at 15:00 , Adam R. Maxwell wrote: > > On Oct 13, 2011, at 00:57 , Fischlin Andreas wrote: > >> AFAIK those services cost a lot. I do not see how that is compatible with an >> open source BibDesk. > > I don't see what on earth you're talking about. We've supported Web of > Science searching in BibDesk for several years, and many (most?) of the web > groups are for-pay sites such as IEEE. > > -- > Adam > > > -- > All the data continuously generated in your IT infrastructure contains a > definitive record of customers, application performance, security > threats, fraudulent activity and more. Splunk takes this data and makes > sense of it. Business sense. IT sense. Common sense. > http://p.sf.net/sfu/splunk-d2d-oct > ___ > Bibdesk-users mailing list > Bibdesk-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/bibdesk-users -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2d-oct ___ Bibdesk-users mailing list Bibdesk-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/bibdesk-users
Re: [Bibdesk-users] Importing PDF files
On Oct 13, 2011, at 00:57 , Fischlin Andreas wrote: > AFAIK those services cost a lot. I do not see how that is compatible with an > open source BibDesk. I don't see what on earth you're talking about. We've supported Web of Science searching in BibDesk for several years, and many (most?) of the web groups are for-pay sites such as IEEE. -- Adam -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2d-oct ___ Bibdesk-users mailing list Bibdesk-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/bibdesk-users
Re: [Bibdesk-users] Cite Key Autogeneration
Container does exactly that for you. You got already the advice. Why don't you
try and see for yourself?
If you don't "believe" us, read the BibDesk help "Browsing References" and the
description of the field Container whether Container is for you.
Regards,
Andreas
ETH Zurich
Prof. Dr. Andreas Fischlin
Systems Ecology - Institute of Integrative Biology
CHN E 21.1
Universitaetstrasse 16
8092 Zurich
SWITZERLAND
andreas.fisch...@env.ethz.ch
www.sysecol.ethz.ch
+41 44 633-6090 phone
+41 44 633-1136 fax
+41 79 221-4657 mobile
Make it as simple as possible, but distrust it!
On 13/10/2011, at 10:14 , Masahiro Takahashi wrote:
> Thanks Andreas,
>
> If I understand correctly, the way you taught is just a normal way.
>
> My question is that if there is a way changing "Container" part
> for different types of references.
>
> I want to set parameters as:
>
> %a1_%f{Journal}_%Y_v%n
> for articles
>
> and
>
> %a1_%f{Booktitle}_%Y_v%n
> for inbook.
>
> Thanks in advance.
>
> Best regards,
> masa
>
> p.s.
> I just recognize that if I set
> %a1_%f{Journal}%f{Booktitle}_%Y_v%n
> then I probably get what I want.
> If there is a better idea or default functionality, please.
>
> On 2011/10/13木, at 16:40, Fischlin Andreas wrote:
>
>> Use %f{Container} to specify how cite keys are generated (menu "BibDesk ->
>> Preferences... -> Cite Key" in the Format String having set the Preset
>> Format to "Custom")
>>
>> and you fill in the fields of the publications the normal way.
>>
>> Regards,
>> Andreas
>>
>>
>> ETH Zurich
>> Prof. Dr. Andreas Fischlin
>> Systems Ecology - Institute of Integrative Biology
>> CHN E 21.1
>> Universitaetstrasse 16
>> 8092 Zurich
>> SWITZERLAND
>>
>> andreas.fisch...@env.ethz.ch
>> www.sysecol.ethz.ch
>>
>> +41 44 633-6090 phone
>> +41 44 633-1136 fax
>> +41 79 221-4657 mobile
>>
>>Make it as simple as possible, but distrust it!
>>
>>
>>
>>
>> On 13/10/2011, at 07:55 , Masahiro Takahashi wrote:
>>
>>> Thank you, Christiaan,
>>>
>>> I need more detailed explanations.
>>> How do I define "Container" for articles and inbook?
You can use %f{Container} for this.
>>>
>>> I checked following link, but I couldn't figured out.
>>> http://bibdesk.sourceforge.net/manual/BibDesk%20Help_91.html#SEC159
>>>
>>> Thank you for your advices in advance.
>>>
>>> Sincerely,
>>> masa
>>>
>>> On 2011/10/11火, at 16:35, Christiaan Hofman wrote:
>>>
On Oct 11, 2011, at 5:31, Masahiro Takahashi wrote:
> Dear all,
>
> I'm using BibDesk with several kinds of materials,
> for example article, inbook, etc...
>
> I'm using "Cite Key Autogeneration" functionality as
>
> %a1_%f{Journal}_%Y_v%n
>
> gives an example of the cite key:
>
> McCracken_Source-Forge_2004_v0
>
> However, for inbook, there is no ENTRY Journal,
> so autogeneration just skip the part.
>
> McCracken__2004_v0
>
> Is there any way of replacing Journal by (for example) Booktitle,
> if there is no ENTRY journal?
> Or is it possible to tell BibDesk use Booktitle for inbook.
>
> Sorry if there is a same question.
>
> Sincerely,
> masa
You can use %f{Container} for this.
Christiaan
>>
>> --
>> All the data continuously generated in your IT infrastructure contains a
>> definitive record of customers, application performance, security
>> threats, fraudulent activity and more. Splunk takes this data and makes
>> sense of it. Business sense. IT sense. Common sense.
>> http://p.sf.net/sfu/splunk-d2d-oct
>> ___
>> Bibdesk-users mailing list
>> Bibdesk-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/bibdesk-users
>
>
> --
> All the data continuously generated in your IT infrastructure contains a
> definitive record of customers, application performance, security
> threats, fraudulent activity and more. Splunk takes this data and makes
> sense of it. Business sense. IT sense. Common sense.
> http://p.sf.net/sfu/splunk-d2d-oct
> ___
> Bibdesk-users mailing list
> Bibdesk-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/bibdesk-users
--
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2d-oct
___
Re: [Bibdesk-users] Cite Key Autogeneration
Thanks Andreas,
If I understand correctly, the way you taught is just a normal way.
My question is that if there is a way changing "Container" part
for different types of references.
I want to set parameters as:
%a1_%f{Journal}_%Y_v%n
for articles
and
%a1_%f{Booktitle}_%Y_v%n
for inbook.
Thanks in advance.
Best regards,
masa
p.s.
I just recognize that if I set
%a1_%f{Journal}%f{Booktitle}_%Y_v%n
then I probably get what I want.
If there is a better idea or default functionality, please.
On 2011/10/13木, at 16:40, Fischlin Andreas wrote:
> Use %f{Container} to specify how cite keys are generated (menu "BibDesk ->
> Preferences... -> Cite Key" in the Format String having set the Preset Format
> to "Custom")
>
> and you fill in the fields of the publications the normal way.
>
> Regards,
> Andreas
>
>
> ETH Zurich
> Prof. Dr. Andreas Fischlin
> Systems Ecology - Institute of Integrative Biology
> CHN E 21.1
> Universitaetstrasse 16
> 8092 Zurich
> SWITZERLAND
>
> andreas.fisch...@env.ethz.ch
> www.sysecol.ethz.ch
>
> +41 44 633-6090 phone
> +41 44 633-1136 fax
> +41 79 221-4657 mobile
>
> Make it as simple as possible, but distrust it!
>
>
>
>
> On 13/10/2011, at 07:55 , Masahiro Takahashi wrote:
>
>> Thank you, Christiaan,
>>
>> I need more detailed explanations.
>> How do I define "Container" for articles and inbook?
>>> You can use %f{Container} for this.
>>
>> I checked following link, but I couldn't figured out.
>> http://bibdesk.sourceforge.net/manual/BibDesk%20Help_91.html#SEC159
>>
>> Thank you for your advices in advance.
>>
>> Sincerely,
>> masa
>>
>> On 2011/10/11火, at 16:35, Christiaan Hofman wrote:
>>
>>>
>>> On Oct 11, 2011, at 5:31, Masahiro Takahashi wrote:
>>>
Dear all,
I'm using BibDesk with several kinds of materials,
for example article, inbook, etc...
I'm using "Cite Key Autogeneration" functionality as
%a1_%f{Journal}_%Y_v%n
gives an example of the cite key:
McCracken_Source-Forge_2004_v0
However, for inbook, there is no ENTRY Journal,
so autogeneration just skip the part.
McCracken__2004_v0
Is there any way of replacing Journal by (for example) Booktitle,
if there is no ENTRY journal?
Or is it possible to tell BibDesk use Booktitle for inbook.
Sorry if there is a same question.
Sincerely,
masa
>>>
>>> You can use %f{Container} for this.
>>>
>>> Christiaan
>>>
>
> --
> All the data continuously generated in your IT infrastructure contains a
> definitive record of customers, application performance, security
> threats, fraudulent activity and more. Splunk takes this data and makes
> sense of it. Business sense. IT sense. Common sense.
> http://p.sf.net/sfu/splunk-d2d-oct
> ___
> Bibdesk-users mailing list
> Bibdesk-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/bibdesk-users
--
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2d-oct
___
Bibdesk-users mailing list
Bibdesk-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/bibdesk-users
Re: [Bibdesk-users] Output format of the bib file
Dear Fabian,
I do not see why your end users are a problem for the solution I suggested as
long as you know what I am talking about. Because you can build all this into a
solution that is as easy as choosing a menu command. That is what I do. I
program it and then I forget, i.e. I get as "dumb" as any other end-user when I
concentrate on something scientific again. This means I use an AppleScript that
is accessible from BibDesk like any other menu command ("Extract
Bibliography"). I guess any end-user of BibDesk can do that, right?
That AppleScript uses templates and sed grep and all sorts of Unix commands in
the post processing shell script that BibDesk so nicely supports (I have
forgotten what it all does). If I remember correctly I use grep to customize my
html output, i.e. setting the title of the web page to something else than the
default. This happens by grepping from a simple text file some of the
parameters used by the AppleScript "Extract Bibliography". But you could also
have a dialog to ask the user, if editing a text file is too difficult for your
end users.
Be welcome to have a look at my BibDesk scripts, which I offer for download
here
http://www.sysecol.ethz.ch/people/afischli/software
together with all templates etc.
Regards,
Andreas
ETH Zurich
Prof. Dr. Andreas Fischlin
Systems Ecology - Institute of Integrative Biology
CHN E 21.1
Universitaetstrasse 16
8092 Zurich
SWITZERLAND
andreas.fisch...@env.ethz.ch
www.sysecol.ethz.ch
+41 44 633-6090 phone
+41 44 633-1136 fax
+41 79 221-4657 mobile
Make it as simple as possible, but distrust it!
On 12/10/2011, at 19:17 , Fabian Dorsch wrote:
> Andreas, Adam, thanks a lot for your quick replies!
>
> My aim is to dynamically display the publications of our research
> group on our Modx website in different and complex ways (e.g.,
> filtered by author, year, keyword, research project, etc.). This is
> why I need a php script, rather than the option of html output from
> BibDesk.
>
> Also, members of the group should be able to add new publications in a
> simple way, i.e. by nothing more complicated than using software like
> BibDesk or JabRef. They are all from the humanities and typically have
> no idea of unix, scripts, etc. - it would just scare them away. This
> is why sed is not an option, either.
>
> I could just use JabRef since it provides the desired output. But it
> doesn't (easily?) allow the user to add custom fields, which are
> needed for the script.
>
> I guess I'll have to continue to look around for a simpler solution.
>
> Fabian
>
>
> On Wed, Oct 12, 2011 at 6:06 PM, Fabian Dorsch
> wrote:
>> Hi,
>>
>> the answer to my question is probably simple, but I couldn't find it
>> myself. I would like to use a script to display references in html.
>> But the script requires a special format of the bibtex entries.
>>
>> When I save my bibliography with BibDesk, each entry looks like this:
>>
>> @article{...
>>...
>>Year = {2007}}
>>
>> But what I need would be this (which is also the output from, say,
>> Google Scholar):
>>
>> @article{...
>>...
>>Year = {2007}
>> }
>>
>> I looked at the preferences of BibDesk, but did not find any way to
>> change this. I also tried out different encodings, with no success.
>> Any suggestions?
>>
>> Thanks a lot!
>>
>> Fabian
>>
>>
>> --
>> www.ideengeschichten.de
>> www.unifr.ch/philo/de/department/modern/dorsch.php
>> www.exre.org
>>
>
>
>
> --
> www.ideengeschichten.de
> www.unifr.ch/philo/de/department/modern/dorsch.php
> www.exre.org
>
> --
> All the data continuously generated in your IT infrastructure contains a
> definitive record of customers, application performance, security
> threats, fraudulent activity and more. Splunk takes this data and makes
> sense of it. Business sense. IT sense. Common sense.
> http://p.sf.net/sfu/splunk-d2d-oct
> ___
> Bibdesk-users mailing list
> Bibdesk-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/bibdesk-users
--
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2d-oct
___
Bibdesk-users mailing list
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Re: [Bibdesk-users] Importing PDF files
AFAIK those services cost a lot. I do not see how that is compatible with an open source BibDesk. Regards, Andreas On 13/10/2011, at 02:35 , Maxwell, Adam R wrote: > > On Oct 12, 2011, at 17:29, Douglas Stebila wrote: > >> On 2011-10-13, at 0:52, "Adam R. Maxwell" wrote: >> >>> AFAIK, none of the screen-scraping sites in the web group are suitable for >>> a query, unfortunately. You need a service such as PubMed or Web of >>> Science with an actual API. >> >> Couldn't you visit the page defined by the DOI, and, if it's a page from a >> site that the web group scrapers know how to scrape, then it scrapes that >> data? Obviously suffers from the limitations of scraping being inaccurate / >> fragile, but it should work a bit. > > Oh, that's a neat idea, and it probably would work. I was thinking you'd > somehow craft a query string for each site, which is harder. > > -- > Adam > > -- > All the data continuously generated in your IT infrastructure contains a > definitive record of customers, application performance, security > threats, fraudulent activity and more. Splunk takes this data and makes > sense of it. Business sense. IT sense. Common sense. > http://p.sf.net/sfu/splunk-d2d-oct___ > Bibdesk-users mailing list > Bibdesk-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/bibdesk-users -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2d-oct ___ Bibdesk-users mailing list Bibdesk-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/bibdesk-users
Re: [Bibdesk-users] Cite Key Autogeneration
Use %f{Container} to specify how cite keys are generated (menu "BibDesk ->
Preferences... -> Cite Key" in the Format String having set the Preset Format
to "Custom")
and you fill in the fields of the publications the normal way.
Regards,
Andreas
ETH Zurich
Prof. Dr. Andreas Fischlin
Systems Ecology - Institute of Integrative Biology
CHN E 21.1
Universitaetstrasse 16
8092 Zurich
SWITZERLAND
andreas.fisch...@env.ethz.ch
www.sysecol.ethz.ch
+41 44 633-6090 phone
+41 44 633-1136 fax
+41 79 221-4657 mobile
Make it as simple as possible, but distrust it!
On 13/10/2011, at 07:55 , Masahiro Takahashi wrote:
> Thank you, Christiaan,
>
> I need more detailed explanations.
> How do I define "Container" for articles and inbook?
>> You can use %f{Container} for this.
>
> I checked following link, but I couldn't figured out.
> http://bibdesk.sourceforge.net/manual/BibDesk%20Help_91.html#SEC159
>
> Thank you for your advices in advance.
>
> Sincerely,
> masa
>
> On 2011/10/11火, at 16:35, Christiaan Hofman wrote:
>
>>
>> On Oct 11, 2011, at 5:31, Masahiro Takahashi wrote:
>>
>>> Dear all,
>>>
>>> I'm using BibDesk with several kinds of materials,
>>> for example article, inbook, etc...
>>>
>>> I'm using "Cite Key Autogeneration" functionality as
>>>
>>> %a1_%f{Journal}_%Y_v%n
>>>
>>> gives an example of the cite key:
>>>
>>> McCracken_Source-Forge_2004_v0
>>>
>>> However, for inbook, there is no ENTRY Journal,
>>> so autogeneration just skip the part.
>>>
>>> McCracken__2004_v0
>>>
>>> Is there any way of replacing Journal by (for example) Booktitle,
>>> if there is no ENTRY journal?
>>> Or is it possible to tell BibDesk use Booktitle for inbook.
>>>
>>> Sorry if there is a same question.
>>>
>>> Sincerely,
>>> masa
>>
>> You can use %f{Container} for this.
>>
>> Christiaan
>>
>>
>> --
>> All the data continuously generated in your IT infrastructure contains a
>> definitive record of customers, application performance, security
>> threats, fraudulent activity and more. Splunk takes this data and makes
>> sense of it. Business sense. IT sense. Common sense.
>> http://p.sf.net/sfu/splunk-d2d-oct
>> ___
>> Bibdesk-users mailing list
>> Bibdesk-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/bibdesk-users
>
>
> --
> All the data continuously generated in your IT infrastructure contains a
> definitive record of customers, application performance, security
> threats, fraudulent activity and more. Splunk takes this data and makes
> sense of it. Business sense. IT sense. Common sense.
> http://p.sf.net/sfu/splunk-d2d-oct
> ___
> Bibdesk-users mailing list
> Bibdesk-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/bibdesk-users
--
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2d-oct
___
Bibdesk-users mailing list
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https://lists.sourceforge.net/lists/listinfo/bibdesk-users
