Re: [O] jabref like orgmode based solution to bibliography management (not for latex)

[John Kitchin]

I cannot reproduce that, and it shouldn't have any effect. Maybe
something else is going on.

>
> Thanks for the quick answer. this does seem to work but as a side effect
> seems to break the TAB key to select action
> the message window shows:
>
> helm-select-nth-action: Nothing is selected
> No Actions available [8 times]
>
> thx again
>
> Z
>
> On Sat, Dec 5, 2015 at 3:05 PM, John Kitchin 
> wrote:
>
>> Try (untested)
>>
>>
>>
>>
>>
>> John
>>
>> ---
>> Professor John Kitchin
>> Doherty Hall A207F
>> Department of Chemical Engineering
>> Carnegie Mellon University
>> Pittsburgh, PA 15213
>> 412-268-7803
>> @johnkitchin
>> http://kitchingroup.cheme.cmu.edu
>>
>>
>> On Sat, Dec 5, 2015 at 7:17 AM, Xebar Saram  wrote:
>>
>>> Hi again Titus and list
>>>
>>> so the semester is finally nearing the end which means i finally have
>>> some time (and a life :)) to get back to what i partially started a few
>>> months ago.
>>>
>>> i have a question regarding Predefined searches. i have a search that
>>> works well for searching papers i authored.
>>> i am thinking of moving towards 2 bib files instead of 1 big one, that is
>>> one for my papers and one for the rest (any disadvantages of using 2 bib
>>> files?).
>>> i want to add in the Predefined search to only draw from my file 
>>> (mypaper.bib),
>>> even though in the default helm-bibtex sources it will have 2 inputs. is
>>> such a thing possible?
>>>
>>> this is how a current search i have looks like
>>>
>>> #+BEGIN_SRC emacs-lisp :results none
>>>
>>>  ;; Define helm-search with predefined search expression:
>>>  (defun helm-bibtex-ikloog-publications ()
>>>"Search BibTeX entries authored by me"
>>>(interactive)
>>>(helm :sources '(helm-source-bibtex)
>>>  :full-frame t
>>>  :input "kloog !unpublished !prep "
>>>  :candidate-number-limit 500))
>>> #+END_SRC
>>>
>>> how does one add the specific .bib file filter?
>>>
>>> best
>>>
>>> Z
>>>
>>> On Sun, May 31, 2015 at 7:23 PM, Titus von der Malsburg <
>>> malsb...@posteo.de> wrote:
>>>

 On 2015-05-31 Sun 03:01, Xebar Saram wrote:
 > Thanks so much everyone for these great replies. i will investigate
 this
 > further today and let everyone know how im going with my transition :)
 >
 > thanks again
 >
 > PS: Titus, do you think  that the helm-bibtex APA style reference list
 > could be user customizable in the future?

 Depends on what you mean by customizable.  If you mean a customization
 option to allows you to replace the function for APA formatting with
 another function, then yes that would definitely make sense.

   Titus

 >
 > Z.
 >
 > On Sat, May 30, 2015 at 6:56 PM, John Kitchin 
 > wrote:
 >
 >>
 >>
 >> On Saturday, May 30, 2015, Titus von der Malsburg 
 >> wrote:
 >>
 >>>
 >>> On 2015-05-30 Sat 01:20, Xebar Saram wrote:
 >>> > Hi all
 >>> >
 >>> > i have been using jabref for the past 2-4 years in my academia
 work to
 >>> > manage my reference library. i dont use latex (..its on my TODO
 >>> list...when
 >>> > (f ever) i have time..) so for now i just want something to manage
 my
 >>> > references. the key things i need to move over from jabref are:
 >>>
 >>> Author of helm-bibtex here.
 >>>
 >>> > 1. easy add references
 >>>
 >>> Helm-bibtex doesn’t deal with this because I prefer to edit my BibTeX
 >>> file by hand.  BibTeX retrieved from journals is almost always messy
 and
 >>> I need to edit it anyway.  It’s not too hard, though: I click on
 BibTeX
 >>> export on the journal page, the BibTeX file is opened in Emacs, I fix
 >>> it, and use a command that appends it to my bibliography.
 >>>
 >>> However, I think org-ref has tools that do more to support importing
 new
 >>> entries and org-ref combines well with helm-bibtex.
 >>
 >>
 >> Org-ref has doi-utils that let you add bibtex entries and download
 PDFs
 >> from a doi or crossref query.
 >>
 >>
 >>>
 >>> > 2. a way to quick filter references (helm bibtex seems like a good
 >>> solution)
 >>>
 >>> That’s what helm-bibtex was written to solve.
 >>>
 >>> > 3. filter lists based on tags/keywords (orgmode has that covered)
 >>>
 >>> In helm-bibtex you can also search for keywords and tags.
 >>>
 >>> > 4. this one is important: a way to quickly export selected
 references in
 >>> > word/odf/html based on a pre fixed style (ie  Nature, Chicago etc)
 >>>
 >>> helm-bibtex can generate references in APA style but as far as I can
 see
 >>> Chicago style is very similar, so it shouldn’t be hard to add support
 >>> for that.
 >>>
 >>> > anyone uses such a system in 

Re: [O] jabref like orgmode based solution to bibliography management (not for latex)

[John Kitchin]

Try (untested)

 (defun helm-bibtex-ikloog-publications ()
   "Search BibTeX entries authored by me"
   (interactive)
(let ((helm-bibtex-bibliography "your special bibfile"))
   (helm :sources '(helm-source-bibtex)
 :full-frame t
 :input "kloog !unpublished !prep "
 :candidate-number-limit 500)))



John

---
Professor John Kitchin
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
@johnkitchin
http://kitchingroup.cheme.cmu.edu


On Sat, Dec 5, 2015 at 7:17 AM, Xebar Saram  wrote:

> Hi again Titus and list
>
> so the semester is finally nearing the end which means i finally have some
> time (and a life :)) to get back to what i partially started a few months
> ago.
>
> i have a question regarding Predefined searches. i have a search that
> works well for searching papers i authored.
> i am thinking of moving towards 2 bib files instead of 1 big one, that is
> one for my papers and one for the rest (any disadvantages of using 2 bib
> files?).
> i want to add in the Predefined search to only draw from my file 
> (mypaper.bib),
> even though in the default helm-bibtex sources it will have 2 inputs. is
> such a thing possible?
>
> this is how a current search i have looks like
>
> #+BEGIN_SRC emacs-lisp :results none
>
>  ;; Define helm-search with predefined search expression:
>  (defun helm-bibtex-ikloog-publications ()
>"Search BibTeX entries authored by me"
>(interactive)
>(helm :sources '(helm-source-bibtex)
>  :full-frame t
>  :input "kloog !unpublished !prep "
>  :candidate-number-limit 500))
> #+END_SRC
>
> how does one add the specific .bib file filter?
>
> best
>
> Z
>
> On Sun, May 31, 2015 at 7:23 PM, Titus von der Malsburg <
> malsb...@posteo.de> wrote:
>
>>
>> On 2015-05-31 Sun 03:01, Xebar Saram wrote:
>> > Thanks so much everyone for these great replies. i will investigate this
>> > further today and let everyone know how im going with my transition :)
>> >
>> > thanks again
>> >
>> > PS: Titus, do you think  that the helm-bibtex APA style reference list
>> > could be user customizable in the future?
>>
>> Depends on what you mean by customizable.  If you mean a customization
>> option to allows you to replace the function for APA formatting with
>> another function, then yes that would definitely make sense.
>>
>>   Titus
>>
>> >
>> > Z.
>> >
>> > On Sat, May 30, 2015 at 6:56 PM, John Kitchin 
>> > wrote:
>> >
>> >>
>> >>
>> >> On Saturday, May 30, 2015, Titus von der Malsburg 
>> >> wrote:
>> >>
>> >>>
>> >>> On 2015-05-30 Sat 01:20, Xebar Saram wrote:
>> >>> > Hi all
>> >>> >
>> >>> > i have been using jabref for the past 2-4 years in my academia work
>> to
>> >>> > manage my reference library. i dont use latex (..its on my TODO
>> >>> list...when
>> >>> > (f ever) i have time..) so for now i just want something to manage
>> my
>> >>> > references. the key things i need to move over from jabref are:
>> >>>
>> >>> Author of helm-bibtex here.
>> >>>
>> >>> > 1. easy add references
>> >>>
>> >>> Helm-bibtex doesn’t deal with this because I prefer to edit my BibTeX
>> >>> file by hand.  BibTeX retrieved from journals is almost always messy
>> and
>> >>> I need to edit it anyway.  It’s not too hard, though: I click on
>> BibTeX
>> >>> export on the journal page, the BibTeX file is opened in Emacs, I fix
>> >>> it, and use a command that appends it to my bibliography.
>> >>>
>> >>> However, I think org-ref has tools that do more to support importing
>> new
>> >>> entries and org-ref combines well with helm-bibtex.
>> >>
>> >>
>> >> Org-ref has doi-utils that let you add bibtex entries and download PDFs
>> >> from a doi or crossref query.
>> >>
>> >>
>> >>>
>> >>> > 2. a way to quick filter references (helm bibtex seems like a good
>> >>> solution)
>> >>>
>> >>> That’s what helm-bibtex was written to solve.
>> >>>
>> >>> > 3. filter lists based on tags/keywords (orgmode has that covered)
>> >>>
>> >>> In helm-bibtex you can also search for keywords and tags.
>> >>>
>> >>> > 4. this one is important: a way to quickly export selected
>> references in
>> >>> > word/odf/html based on a pre fixed style (ie  Nature, Chicago etc)
>> >>>
>> >>> helm-bibtex can generate references in APA style but as far as I can
>> see
>> >>> Chicago style is very similar, so it shouldn’t be hard to add support
>> >>> for that.
>> >>>
>> >>> > anyone uses such a system in emacs/org and can recommend the way to
>> >>> > go?
>> >>>
>> >>> For more details, see: https://github.com/tmalsburg/helm-bibtex
>> >>>
>> >>>   Titus
>> >>>
>> >>>
>> >>
>> >> --
>> >> John
>> >>
>> >> ---
>> >> Professor John Kitchin
>> >> Doherty Hall A207F
>> >> Department of Chemical Engineering
>> >> Carnegie Mellon University
>> >> Pittsburgh, PA 15213
>> >> 412-268-7803
>> >> @johnkitchin
>> >> 

Re: [O] jabref like orgmode based solution to bibliography management (not for latex)

[Xebar Saram]

Hi John

Thanks for the quick answer. this does seem to work but as a side effect
seems to break the TAB key to select action
the message window shows:

helm-select-nth-action: Nothing is selected
No Actions available [8 times]

thx again

Z

On Sat, Dec 5, 2015 at 3:05 PM, John Kitchin 
wrote:

> Try (untested)
>
>  (defun helm-bibtex-ikloog-publications ()
>"Search BibTeX entries authored by me"
>(interactive)
> (let ((helm-bibtex-bibliography "your special bibfile"))
>(helm :sources '(helm-source-bibtex)
>  :full-frame t
>  :input "kloog !unpublished !prep "
>  :candidate-number-limit 500)))
>
>
>
> John
>
> ---
> Professor John Kitchin
> Doherty Hall A207F
> Department of Chemical Engineering
> Carnegie Mellon University
> Pittsburgh, PA 15213
> 412-268-7803
> @johnkitchin
> http://kitchingroup.cheme.cmu.edu
>
>
> On Sat, Dec 5, 2015 at 7:17 AM, Xebar Saram  wrote:
>
>> Hi again Titus and list
>>
>> so the semester is finally nearing the end which means i finally have
>> some time (and a life :)) to get back to what i partially started a few
>> months ago.
>>
>> i have a question regarding Predefined searches. i have a search that
>> works well for searching papers i authored.
>> i am thinking of moving towards 2 bib files instead of 1 big one, that is
>> one for my papers and one for the rest (any disadvantages of using 2 bib
>> files?).
>> i want to add in the Predefined search to only draw from my file 
>> (mypaper.bib),
>> even though in the default helm-bibtex sources it will have 2 inputs. is
>> such a thing possible?
>>
>> this is how a current search i have looks like
>>
>> #+BEGIN_SRC emacs-lisp :results none
>>
>>  ;; Define helm-search with predefined search expression:
>>  (defun helm-bibtex-ikloog-publications ()
>>"Search BibTeX entries authored by me"
>>(interactive)
>>(helm :sources '(helm-source-bibtex)
>>  :full-frame t
>>  :input "kloog !unpublished !prep "
>>  :candidate-number-limit 500))
>> #+END_SRC
>>
>> how does one add the specific .bib file filter?
>>
>> best
>>
>> Z
>>
>> On Sun, May 31, 2015 at 7:23 PM, Titus von der Malsburg <
>> malsb...@posteo.de> wrote:
>>
>>>
>>> On 2015-05-31 Sun 03:01, Xebar Saram wrote:
>>> > Thanks so much everyone for these great replies. i will investigate
>>> this
>>> > further today and let everyone know how im going with my transition :)
>>> >
>>> > thanks again
>>> >
>>> > PS: Titus, do you think  that the helm-bibtex APA style reference list
>>> > could be user customizable in the future?
>>>
>>> Depends on what you mean by customizable.  If you mean a customization
>>> option to allows you to replace the function for APA formatting with
>>> another function, then yes that would definitely make sense.
>>>
>>>   Titus
>>>
>>> >
>>> > Z.
>>> >
>>> > On Sat, May 30, 2015 at 6:56 PM, John Kitchin >> >
>>> > wrote:
>>> >
>>> >>
>>> >>
>>> >> On Saturday, May 30, 2015, Titus von der Malsburg >> >
>>> >> wrote:
>>> >>
>>> >>>
>>> >>> On 2015-05-30 Sat 01:20, Xebar Saram wrote:
>>> >>> > Hi all
>>> >>> >
>>> >>> > i have been using jabref for the past 2-4 years in my academia
>>> work to
>>> >>> > manage my reference library. i dont use latex (..its on my TODO
>>> >>> list...when
>>> >>> > (f ever) i have time..) so for now i just want something to manage
>>> my
>>> >>> > references. the key things i need to move over from jabref are:
>>> >>>
>>> >>> Author of helm-bibtex here.
>>> >>>
>>> >>> > 1. easy add references
>>> >>>
>>> >>> Helm-bibtex doesn’t deal with this because I prefer to edit my BibTeX
>>> >>> file by hand.  BibTeX retrieved from journals is almost always messy
>>> and
>>> >>> I need to edit it anyway.  It’s not too hard, though: I click on
>>> BibTeX
>>> >>> export on the journal page, the BibTeX file is opened in Emacs, I fix
>>> >>> it, and use a command that appends it to my bibliography.
>>> >>>
>>> >>> However, I think org-ref has tools that do more to support importing
>>> new
>>> >>> entries and org-ref combines well with helm-bibtex.
>>> >>
>>> >>
>>> >> Org-ref has doi-utils that let you add bibtex entries and download
>>> PDFs
>>> >> from a doi or crossref query.
>>> >>
>>> >>
>>> >>>
>>> >>> > 2. a way to quick filter references (helm bibtex seems like a good
>>> >>> solution)
>>> >>>
>>> >>> That’s what helm-bibtex was written to solve.
>>> >>>
>>> >>> > 3. filter lists based on tags/keywords (orgmode has that covered)
>>> >>>
>>> >>> In helm-bibtex you can also search for keywords and tags.
>>> >>>
>>> >>> > 4. this one is important: a way to quickly export selected
>>> references in
>>> >>> > word/odf/html based on a pre fixed style (ie  Nature, Chicago etc)
>>> >>>
>>> >>> helm-bibtex can generate references in APA style but as far as I can
>>> see
>>> >>> Chicago style is very similar, so it shouldn’t be hard to add support

Re: [O] jabref like orgmode based solution to bibliography management (not for latex)

[Xebar Saram]

Hi Guys

I have no clue why i had the issue before but after an emacs restart Johns
code snippet does work :D

thanks again guys, really appreciate your help as always

kind regards

Z

On Sat, Dec 5, 2015 at 8:04 PM, Titus von der Malsburg 
wrote:

>
> John’s code should do the trick.  I don’t see how this could possibly
> cause your problems with the action menu.  The change should be
> completely transparent for Helm.
>
> Regarding your other question: I don’t see any disadvantages of using
> several BibTeX files but I also don’t see an advantage because
> helm-bibtex gives you all you need to select your own publications with
> just a few key strokes.  If helm-bibtex’ search does not work well in
> your case (perhaps another author has the same name as you), I would
> suggest using tags to mark your own publications:
>
>   https://github.com/tmalsburg/helm-bibtex#tagging-publications
>
> Titus
>
>
> On 2015-12-05 Sat 05:31, John Kitchin wrote:
> > I cannot reproduce that, and it shouldn't have any effect. Maybe
> > something else is going on.
> >
> >>
> >> Thanks for the quick answer. this does seem to work but as a side effect
> >> seems to break the TAB key to select action
> >> the message window shows:
> >>
> >> helm-select-nth-action: Nothing is selected
> >> No Actions available [8 times]
> >>
> >> thx again
> >>
> >> Z
> >>
> >> On Sat, Dec 5, 2015 at 3:05 PM, John Kitchin 
> >> wrote:
> >>
> >>> Try (untested)
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> John
> >>>
> >>> ---
> >>> Professor John Kitchin
> >>> Doherty Hall A207F
> >>> Department of Chemical Engineering
> >>> Carnegie Mellon University
> >>> Pittsburgh, PA 15213
> >>> 412-268-7803
> >>> @johnkitchin
> >>> http://kitchingroup.cheme.cmu.edu
> >>>
> >>>
> >>> On Sat, Dec 5, 2015 at 7:17 AM, Xebar Saram  wrote:
> >>>
>  Hi again Titus and list
> 
>  so the semester is finally nearing the end which means i finally have
>  some time (and a life :)) to get back to what i partially started a
> few
>  months ago.
> 
>  i have a question regarding Predefined searches. i have a search that
>  works well for searching papers i authored.
>  i am thinking of moving towards 2 bib files instead of 1 big one,
> that is
>  one for my papers and one for the rest (any disadvantages of using 2
> bib
>  files?).
>  i want to add in the Predefined search to only draw from my file
> (mypaper.bib),
>  even though in the default helm-bibtex sources it will have 2 inputs.
> is
>  such a thing possible?
> 
>  this is how a current search i have looks like
> 
>  #+BEGIN_SRC emacs-lisp :results none
> 
>   ;; Define helm-search with predefined search expression:
>   (defun helm-bibtex-ikloog-publications ()
> "Search BibTeX entries authored by me"
> (interactive)
> (helm :sources '(helm-source-bibtex)
>   :full-frame t
>   :input "kloog !unpublished !prep "
>   :candidate-number-limit 500))
>  #+END_SRC
> 
>  how does one add the specific .bib file filter?
> 
>  best
> 
>  Z
> 
>  On Sun, May 31, 2015 at 7:23 PM, Titus von der Malsburg <
>  malsb...@posteo.de> wrote:
> 
> >
> > On 2015-05-31 Sun 03:01, Xebar Saram wrote:
> > > Thanks so much everyone for these great replies. i will investigate
> > this
> > > further today and let everyone know how im going with my
> transition :)
> > >
> > > thanks again
> > >
> > > PS: Titus, do you think  that the helm-bibtex APA style reference
> list
> > > could be user customizable in the future?
> >
> > Depends on what you mean by customizable.  If you mean a
> customization
> > option to allows you to replace the function for APA formatting with
> > another function, then yes that would definitely make sense.
> >
> >   Titus
> >
> > >
> > > Z.
> > >
> > > On Sat, May 30, 2015 at 6:56 PM, John Kitchin <
> jkitc...@andrew.cmu.edu
> > >
> > > wrote:
> > >
> > >>
> > >>
> > >> On Saturday, May 30, 2015, Titus von der Malsburg <
> malsb...@posteo.de
> > >
> > >> wrote:
> > >>
> > >>>
> > >>> On 2015-05-30 Sat 01:20, Xebar Saram wrote:
> > >>> > Hi all
> > >>> >
> > >>> > i have been using jabref for the past 2-4 years in my academia
> > work to
> > >>> > manage my reference library. i dont use latex (..its on my TODO
> > >>> list...when
> > >>> > (f ever) i have time..) so for now i just want something to
> manage
> > my
> > >>> > references. the key things i need to move over from jabref are:
> > >>>
> > >>> Author of helm-bibtex here.
> > >>>
> > >>> > 1. easy add references
> > >>>
> > >>> Helm-bibtex doesn’t deal with this because I prefer to edit my
> BibTeX
> 

Re: [O] jabref like orgmode based solution to bibliography management (not for latex)

[Titus von der Malsburg]

John’s code should do the trick.  I don’t see how this could possibly
cause your problems with the action menu.  The change should be
completely transparent for Helm.

Regarding your other question: I don’t see any disadvantages of using
several BibTeX files but I also don’t see an advantage because
helm-bibtex gives you all you need to select your own publications with
just a few key strokes.  If helm-bibtex’ search does not work well in
your case (perhaps another author has the same name as you), I would
suggest using tags to mark your own publications:

  https://github.com/tmalsburg/helm-bibtex#tagging-publications

Titus


On 2015-12-05 Sat 05:31, John Kitchin wrote:
> I cannot reproduce that, and it shouldn't have any effect. Maybe
> something else is going on.
>
>>
>> Thanks for the quick answer. this does seem to work but as a side effect
>> seems to break the TAB key to select action
>> the message window shows:
>>
>> helm-select-nth-action: Nothing is selected
>> No Actions available [8 times]
>>
>> thx again
>>
>> Z
>>
>> On Sat, Dec 5, 2015 at 3:05 PM, John Kitchin 
>> wrote:
>>
>>> Try (untested)
>>>
>>>
>>>
>>>
>>>
>>> John
>>>
>>> ---
>>> Professor John Kitchin
>>> Doherty Hall A207F
>>> Department of Chemical Engineering
>>> Carnegie Mellon University
>>> Pittsburgh, PA 15213
>>> 412-268-7803
>>> @johnkitchin
>>> http://kitchingroup.cheme.cmu.edu
>>>
>>>
>>> On Sat, Dec 5, 2015 at 7:17 AM, Xebar Saram  wrote:
>>>
 Hi again Titus and list

 so the semester is finally nearing the end which means i finally have
 some time (and a life :)) to get back to what i partially started a few
 months ago.

 i have a question regarding Predefined searches. i have a search that
 works well for searching papers i authored.
 i am thinking of moving towards 2 bib files instead of 1 big one, that is
 one for my papers and one for the rest (any disadvantages of using 2 bib
 files?).
 i want to add in the Predefined search to only draw from my file 
 (mypaper.bib),
 even though in the default helm-bibtex sources it will have 2 inputs. is
 such a thing possible?

 this is how a current search i have looks like

 #+BEGIN_SRC emacs-lisp :results none

  ;; Define helm-search with predefined search expression:
  (defun helm-bibtex-ikloog-publications ()
"Search BibTeX entries authored by me"
(interactive)
(helm :sources '(helm-source-bibtex)
  :full-frame t
  :input "kloog !unpublished !prep "
  :candidate-number-limit 500))
 #+END_SRC

 how does one add the specific .bib file filter?

 best

 Z

 On Sun, May 31, 2015 at 7:23 PM, Titus von der Malsburg <
 malsb...@posteo.de> wrote:

>
> On 2015-05-31 Sun 03:01, Xebar Saram wrote:
> > Thanks so much everyone for these great replies. i will investigate
> this
> > further today and let everyone know how im going with my transition :)
> >
> > thanks again
> >
> > PS: Titus, do you think  that the helm-bibtex APA style reference list
> > could be user customizable in the future?
>
> Depends on what you mean by customizable.  If you mean a customization
> option to allows you to replace the function for APA formatting with
> another function, then yes that would definitely make sense.
>
>   Titus
>
> >
> > Z.
> >
> > On Sat, May 30, 2015 at 6:56 PM, John Kitchin  >
> > wrote:
> >
> >>
> >>
> >> On Saturday, May 30, 2015, Titus von der Malsburg  >
> >> wrote:
> >>
> >>>
> >>> On 2015-05-30 Sat 01:20, Xebar Saram wrote:
> >>> > Hi all
> >>> >
> >>> > i have been using jabref for the past 2-4 years in my academia
> work to
> >>> > manage my reference library. i dont use latex (..its on my TODO
> >>> list...when
> >>> > (f ever) i have time..) so for now i just want something to manage
> my
> >>> > references. the key things i need to move over from jabref are:
> >>>
> >>> Author of helm-bibtex here.
> >>>
> >>> > 1. easy add references
> >>>
> >>> Helm-bibtex doesn’t deal with this because I prefer to edit my BibTeX
> >>> file by hand.  BibTeX retrieved from journals is almost always messy
> and
> >>> I need to edit it anyway.  It’s not too hard, though: I click on
> BibTeX
> >>> export on the journal page, the BibTeX file is opened in Emacs, I fix
> >>> it, and use a command that appends it to my bibliography.
> >>>
> >>> However, I think org-ref has tools that do more to support importing
> new
> >>> entries and org-ref combines well with helm-bibtex.
> >>
> >>
> >> Org-ref has doi-utils that let you add bibtex entries and 

Re: [O] jabref like orgmode based solution to bibliography management (not for latex)

[Xebar Saram]

Hi again Titus and list

so the semester is finally nearing the end which means i finally have some
time (and a life :)) to get back to what i partially started a few months
ago.

i have a question regarding Predefined searches. i have a search that works
well for searching papers i authored.
i am thinking of moving towards 2 bib files instead of 1 big one, that is
one for my papers and one for the rest (any disadvantages of using 2 bib
files?).
i want to add in the Predefined search to only draw from my file (mypaper.bib),
even though in the default helm-bibtex sources it will have 2 inputs. is
such a thing possible?

this is how a current search i have looks like

#+BEGIN_SRC emacs-lisp :results none

 ;; Define helm-search with predefined search expression:
 (defun helm-bibtex-ikloog-publications ()
   "Search BibTeX entries authored by me"
   (interactive)
   (helm :sources '(helm-source-bibtex)
 :full-frame t
 :input "kloog !unpublished !prep "
 :candidate-number-limit 500))
#+END_SRC

how does one add the specific .bib file filter?

best

Z

On Sun, May 31, 2015 at 7:23 PM, Titus von der Malsburg 
wrote:

>
> On 2015-05-31 Sun 03:01, Xebar Saram wrote:
> > Thanks so much everyone for these great replies. i will investigate this
> > further today and let everyone know how im going with my transition :)
> >
> > thanks again
> >
> > PS: Titus, do you think  that the helm-bibtex APA style reference list
> > could be user customizable in the future?
>
> Depends on what you mean by customizable.  If you mean a customization
> option to allows you to replace the function for APA formatting with
> another function, then yes that would definitely make sense.
>
>   Titus
>
> >
> > Z.
> >
> > On Sat, May 30, 2015 at 6:56 PM, John Kitchin 
> > wrote:
> >
> >>
> >>
> >> On Saturday, May 30, 2015, Titus von der Malsburg 
> >> wrote:
> >>
> >>>
> >>> On 2015-05-30 Sat 01:20, Xebar Saram wrote:
> >>> > Hi all
> >>> >
> >>> > i have been using jabref for the past 2-4 years in my academia work
> to
> >>> > manage my reference library. i dont use latex (..its on my TODO
> >>> list...when
> >>> > (f ever) i have time..) so for now i just want something to manage my
> >>> > references. the key things i need to move over from jabref are:
> >>>
> >>> Author of helm-bibtex here.
> >>>
> >>> > 1. easy add references
> >>>
> >>> Helm-bibtex doesn’t deal with this because I prefer to edit my BibTeX
> >>> file by hand.  BibTeX retrieved from journals is almost always messy
> and
> >>> I need to edit it anyway.  It’s not too hard, though: I click on BibTeX
> >>> export on the journal page, the BibTeX file is opened in Emacs, I fix
> >>> it, and use a command that appends it to my bibliography.
> >>>
> >>> However, I think org-ref has tools that do more to support importing
> new
> >>> entries and org-ref combines well with helm-bibtex.
> >>
> >>
> >> Org-ref has doi-utils that let you add bibtex entries and download PDFs
> >> from a doi or crossref query.
> >>
> >>
> >>>
> >>> > 2. a way to quick filter references (helm bibtex seems like a good
> >>> solution)
> >>>
> >>> That’s what helm-bibtex was written to solve.
> >>>
> >>> > 3. filter lists based on tags/keywords (orgmode has that covered)
> >>>
> >>> In helm-bibtex you can also search for keywords and tags.
> >>>
> >>> > 4. this one is important: a way to quickly export selected
> references in
> >>> > word/odf/html based on a pre fixed style (ie  Nature, Chicago etc)
> >>>
> >>> helm-bibtex can generate references in APA style but as far as I can
> see
> >>> Chicago style is very similar, so it shouldn’t be hard to add support
> >>> for that.
> >>>
> >>> > anyone uses such a system in emacs/org and can recommend the way to
> >>> > go?
> >>>
> >>> For more details, see: https://github.com/tmalsburg/helm-bibtex
> >>>
> >>>   Titus
> >>>
> >>>
> >>
> >> --
> >> John
> >>
> >> ---
> >> Professor John Kitchin
> >> Doherty Hall A207F
> >> Department of Chemical Engineering
> >> Carnegie Mellon University
> >> Pittsburgh, PA 15213
> >> 412-268-7803
> >> @johnkitchin
> >> http://kitchingroup.cheme.cmu.edu
> >>
> >>
> >>
>
>

Re: [O] jabref like orgmode based solution to bibliography management (not for latex)

[Titus von der Malsburg]

On 2015-05-31 Sun 03:01, Xebar Saram wrote:
 Thanks so much everyone for these great replies. i will investigate this
 further today and let everyone know how im going with my transition :)

 thanks again

 PS: Titus, do you think  that the helm-bibtex APA style reference list
 could be user customizable in the future?

Depends on what you mean by customizable.  If you mean a customization
option to allows you to replace the function for APA formatting with
another function, then yes that would definitely make sense.

  Titus


 Z.

 On Sat, May 30, 2015 at 6:56 PM, John Kitchin jkitc...@andrew.cmu.edu
 wrote:



 On Saturday, May 30, 2015, Titus von der Malsburg malsb...@posteo.de
 wrote:


 On 2015-05-30 Sat 01:20, Xebar Saram wrote:
  Hi all
 
  i have been using jabref for the past 2-4 years in my academia work to
  manage my reference library. i dont use latex (..its on my TODO
 list...when
  (f ever) i have time..) so for now i just want something to manage my
  references. the key things i need to move over from jabref are:

 Author of helm-bibtex here.

  1. easy add references

 Helm-bibtex doesn’t deal with this because I prefer to edit my BibTeX
 file by hand.  BibTeX retrieved from journals is almost always messy and
 I need to edit it anyway.  It’s not too hard, though: I click on BibTeX
 export on the journal page, the BibTeX file is opened in Emacs, I fix
 it, and use a command that appends it to my bibliography.

 However, I think org-ref has tools that do more to support importing new
 entries and org-ref combines well with helm-bibtex.


 Org-ref has doi-utils that let you add bibtex entries and download PDFs
 from a doi or crossref query.



  2. a way to quick filter references (helm bibtex seems like a good
 solution)

 That’s what helm-bibtex was written to solve.

  3. filter lists based on tags/keywords (orgmode has that covered)

 In helm-bibtex you can also search for keywords and tags.

  4. this one is important: a way to quickly export selected references in
  word/odf/html based on a pre fixed style (ie  Nature, Chicago etc)

 helm-bibtex can generate references in APA style but as far as I can see
 Chicago style is very similar, so it shouldn’t be hard to add support
 for that.

  anyone uses such a system in emacs/org and can recommend the way to
  go?

 For more details, see: https://github.com/tmalsburg/helm-bibtex

   Titus



 --
 John

 ---
 Professor John Kitchin
 Doherty Hall A207F
 Department of Chemical Engineering
 Carnegie Mellon University
 Pittsburgh, PA 15213
 412-268-7803
 @johnkitchin
 http://kitchingroup.cheme.cmu.edu






signature.asc
Description: PGP signature

Re: [O] jabref like orgmode based solution to bibliography management (not for latex)

[Xebar Saram]

Thanks so much everyone for these great replies. i will investigate this
further today and let everyone know how im going with my transition :)

thanks again

PS: Titus, do you think  that the helm-bibtex APA style reference list
could be user customizable in the future?

Z.

On Sat, May 30, 2015 at 6:56 PM, John Kitchin jkitc...@andrew.cmu.edu
wrote:



 On Saturday, May 30, 2015, Titus von der Malsburg malsb...@posteo.de
 wrote:


 On 2015-05-30 Sat 01:20, Xebar Saram wrote:
  Hi all
 
  i have been using jabref for the past 2-4 years in my academia work to
  manage my reference library. i dont use latex (..its on my TODO
 list...when
  (f ever) i have time..) so for now i just want something to manage my
  references. the key things i need to move over from jabref are:

 Author of helm-bibtex here.

  1. easy add references

 Helm-bibtex doesn’t deal with this because I prefer to edit my BibTeX
 file by hand.  BibTeX retrieved from journals is almost always messy and
 I need to edit it anyway.  It’s not too hard, though: I click on BibTeX
 export on the journal page, the BibTeX file is opened in Emacs, I fix
 it, and use a command that appends it to my bibliography.

 However, I think org-ref has tools that do more to support importing new
 entries and org-ref combines well with helm-bibtex.


 Org-ref has doi-utils that let you add bibtex entries and download PDFs
 from a doi or crossref query.



  2. a way to quick filter references (helm bibtex seems like a good
 solution)

 That’s what helm-bibtex was written to solve.

  3. filter lists based on tags/keywords (orgmode has that covered)

 In helm-bibtex you can also search for keywords and tags.

  4. this one is important: a way to quickly export selected references in
  word/odf/html based on a pre fixed style (ie  Nature, Chicago etc)

 helm-bibtex can generate references in APA style but as far as I can see
 Chicago style is very similar, so it shouldn’t be hard to add support
 for that.

  anyone uses such a system in emacs/org and can recommend the way to
  go?

 For more details, see: https://github.com/tmalsburg/helm-bibtex

   Titus



 --
 John

 ---
 Professor John Kitchin
 Doherty Hall A207F
 Department of Chemical Engineering
 Carnegie Mellon University
 Pittsburgh, PA 15213
 412-268-7803
 @johnkitchin
 http://kitchingroup.cheme.cmu.edu

Re: [O] jabref like orgmode based solution to bibliography management (not for latex)

[John Kitchin]

Org-ref also has some customizable formatting. It is pretty basic but
customizable.

On Sunday, May 31, 2015, Xebar Saram zelt...@gmail.com wrote:

 Thanks so much everyone for these great replies. i will investigate this
 further today and let everyone know how im going with my transition :)

 thanks again

 PS: Titus, do you think  that the helm-bibtex APA style reference list
 could be user customizable in the future?

 Z.

 On Sat, May 30, 2015 at 6:56 PM, John Kitchin jkitc...@andrew.cmu.edu
 javascript:_e(%7B%7D,'cvml','jkitc...@andrew.cmu.edu'); wrote:



 On Saturday, May 30, 2015, Titus von der Malsburg malsb...@posteo.de
 javascript:_e(%7B%7D,'cvml','malsb...@posteo.de'); wrote:


 On 2015-05-30 Sat 01:20, Xebar Saram wrote:
  Hi all
 
  i have been using jabref for the past 2-4 years in my academia work to
  manage my reference library. i dont use latex (..its on my TODO
 list...when
  (f ever) i have time..) so for now i just want something to manage my
  references. the key things i need to move over from jabref are:

 Author of helm-bibtex here.

  1. easy add references

 Helm-bibtex doesn’t deal with this because I prefer to edit my BibTeX
 file by hand.  BibTeX retrieved from journals is almost always messy and
 I need to edit it anyway.  It’s not too hard, though: I click on BibTeX
 export on the journal page, the BibTeX file is opened in Emacs, I fix
 it, and use a command that appends it to my bibliography.

 However, I think org-ref has tools that do more to support importing new
 entries and org-ref combines well with helm-bibtex.


 Org-ref has doi-utils that let you add bibtex entries and download PDFs
 from a doi or crossref query.



  2. a way to quick filter references (helm bibtex seems like a good
 solution)

 That’s what helm-bibtex was written to solve.

  3. filter lists based on tags/keywords (orgmode has that covered)

 In helm-bibtex you can also search for keywords and tags.

  4. this one is important: a way to quickly export selected references
 in
  word/odf/html based on a pre fixed style (ie  Nature, Chicago etc)

 helm-bibtex can generate references in APA style but as far as I can see
 Chicago style is very similar, so it shouldn’t be hard to add support
 for that.

  anyone uses such a system in emacs/org and can recommend the way to
  go?

 For more details, see: https://github.com/tmalsburg/helm-bibtex

   Titus



 --
 John

 ---
 Professor John Kitchin
 Doherty Hall A207F
 Department of Chemical Engineering
 Carnegie Mellon University
 Pittsburgh, PA 15213
 412-268-7803
 @johnkitchin
 http://kitchingroup.cheme.cmu.edu





-- 
John

---
Professor John Kitchin
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
@johnkitchin
http://kitchingroup.cheme.cmu.edu

Re: [O] jabref like orgmode based solution to bibliography management (not for latex)

[Vaidheeswaran C]

On Saturday 30 May 2015 01:50 PM, Xebar Saram wrote:

 4. this one is important: a way to quickly export selected references in
 word/odf/html based on a pre fixed style (ie  Nature, Chicago etc)

You may have to move to new citation syntax on my private repo.

See http://repo.or.cz/w/org-mode/org-cv.git

The example org and odt files are available in this post:
http://lists.gnu.org/archive/html/emacs-orgmode/2015-03/msg00451.html
The documentation is in ox-jabref.el

If you report issues, I will address them promptly.

Re: [O] jabref like orgmode based solution to bibliography management (not for latex)

[Otto Pichlhöfer]

Xebar Saram zeltakc at gmail.com writes:

 4. this one is important: a way to quickly export selected references in 
word/odf/html based on a pre fixed style (ie  Nature, Chicago etc)

You might want to finish up the citations after the paper is exported. 
Have a look at 
http://www.docear.org/software/add-ons/docear4word/overview/

Regards,
Otto

Re: [O] jabref like orgmode based solution to bibliography management (not for latex)

[Titus von der Malsburg]

On 2015-05-30 Sat 01:20, Xebar Saram wrote:
 Hi all

 i have been using jabref for the past 2-4 years in my academia work to
 manage my reference library. i dont use latex (..its on my TODO list...when
 (f ever) i have time..) so for now i just want something to manage my
 references. the key things i need to move over from jabref are:

Author of helm-bibtex here.

 1. easy add references

Helm-bibtex doesn’t deal with this because I prefer to edit my BibTeX
file by hand.  BibTeX retrieved from journals is almost always messy and
I need to edit it anyway.  It’s not too hard, though: I click on BibTeX
export on the journal page, the BibTeX file is opened in Emacs, I fix
it, and use a command that appends it to my bibliography.

However, I think org-ref has tools that do more to support importing new
entries and org-ref combines well with helm-bibtex.

 2. a way to quick filter references (helm bibtex seems like a good solution)

That’s what helm-bibtex was written to solve.

 3. filter lists based on tags/keywords (orgmode has that covered)

In helm-bibtex you can also search for keywords and tags. 

 4. this one is important: a way to quickly export selected references in
 word/odf/html based on a pre fixed style (ie  Nature, Chicago etc)

helm-bibtex can generate references in APA style but as far as I can see
Chicago style is very similar, so it shouldn’t be hard to add support
for that.

 anyone uses such a system in emacs/org and can recommend the way to
 go?

For more details, see: https://github.com/tmalsburg/helm-bibtex

  Titus



signature.asc
Description: PGP signature

Re: [O] jabref like orgmode based solution to bibliography management (not for latex)

[John Kitchin]

On Saturday, May 30, 2015, Titus von der Malsburg malsb...@posteo.de
wrote:


 On 2015-05-30 Sat 01:20, Xebar Saram wrote:
  Hi all
 
  i have been using jabref for the past 2-4 years in my academia work to
  manage my reference library. i dont use latex (..its on my TODO
 list...when
  (f ever) i have time..) so for now i just want something to manage my
  references. the key things i need to move over from jabref are:

 Author of helm-bibtex here.

  1. easy add references

 Helm-bibtex doesn’t deal with this because I prefer to edit my BibTeX
 file by hand.  BibTeX retrieved from journals is almost always messy and
 I need to edit it anyway.  It’s not too hard, though: I click on BibTeX
 export on the journal page, the BibTeX file is opened in Emacs, I fix
 it, and use a command that appends it to my bibliography.

 However, I think org-ref has tools that do more to support importing new
 entries and org-ref combines well with helm-bibtex.


Org-ref has doi-utils that let you add bibtex entries and download PDFs
from a doi or crossref query.



  2. a way to quick filter references (helm bibtex seems like a good
 solution)

 That’s what helm-bibtex was written to solve.

  3. filter lists based on tags/keywords (orgmode has that covered)

 In helm-bibtex you can also search for keywords and tags.

  4. this one is important: a way to quickly export selected references in
  word/odf/html based on a pre fixed style (ie  Nature, Chicago etc)

 helm-bibtex can generate references in APA style but as far as I can see
 Chicago style is very similar, so it shouldn’t be hard to add support
 for that.

  anyone uses such a system in emacs/org and can recommend the way to
  go?

 For more details, see: https://github.com/tmalsburg/helm-bibtex

   Titus



-- 
John

---
Professor John Kitchin
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
@johnkitchin
http://kitchingroup.cheme.cmu.edu