The ability to add references would probably not be too difficult. Editing is a more complex issue. Would the former be satisfactory or not sufficient to be worth the effort?
Jon
Sonny Software
Bookends Server-based Collaboration
Bookends server-based collaboration
I agree wholeheartedly with ozean. This feature would be near the top of my list—I'd even be willing to pay more for it.
One indicator of demand for this feature may be the popularity of services like CiteULike and Connotea. These service provide a way to manage and share references online, but there are some real limitations as compared to what Bookends could offer by allowing users to edit databases online. For example, Bookends' ability to serve PDFs in addition to citations would be enormously valuable for my research team—not to mention for teaching. The ability to work with multiple databases also is a big strength over something like CiteULike.
Jon: you indicated that the ability to add references would probably not be too difficult. In the near term, that would be enough to allow me to set up the server for my collaborators. Editing would certainly be nice down the road, but just adding references would be terrific.
One indicator of demand for this feature may be the popularity of services like CiteULike and Connotea. These service provide a way to manage and share references online, but there are some real limitations as compared to what Bookends could offer by allowing users to edit databases online. For example, Bookends' ability to serve PDFs in addition to citations would be enormously valuable for my research team—not to mention for teaching. The ability to work with multiple databases also is a big strength over something like CiteULike.
Jon: you indicated that the ability to add references would probably not be too difficult. In the near term, that would be enough to allow me to set up the server for my collaborators. Editing would certainly be nice down the road, but just adding references would be terrific.
There are a number of ways one could envision this.
One would be to simply let users create a form that would have the author, title, etc and submit it to Bookends. Anyone could do this via the web (password protectable, of course).
Another would be to let users submit a reference directly from a Bookends database. This would be browser-independent, but would require that the user be using Bookends.
The first is more universal but ugly. The second is more restrictive but slicker.
Any thoughts (or other options)?
Jon
Sonny Software
One would be to simply let users create a form that would have the author, title, etc and submit it to Bookends. Anyone could do this via the web (password protectable, of course).
Another would be to let users submit a reference directly from a Bookends database. This would be browser-independent, but would require that the user be using Bookends.
The first is more universal but ugly. The second is more restrictive but slicker.
Any thoughts (or other options)?
Jon
Sonny Software
While both would certainly be nice, if I have to choose I'd vote for the second. Most situations where this would make sense to me involves several people working on the same manuscript. In this case all should really be using bookends anyway for this to be really helpful...Jon wrote:
The first is more universal but ugly. The second is more restrictive but slicker.
Any thoughts (or other options)?
Would that work outside a local network too?
I would favor the universal but ugly option. Most of my collaborators live in a Windows world (as did I until six months ago), so using Bookends is not an option for them. I would be most excited about a platform-independent option for adding references.The first is more universal but ugly. The second is more restrictive but slicker.
Any thoughts (or other options)?
I can envision other uses for this feature besides working together on a manuscript. For example, I'm setting up a wiki for my lab, and it would be useful to have a central database that my graduate students could access and update. It would also be useful to collaborate with colleagues at other institutions to identify important new literature in a particular area or related to a particular project.
Perhaps a third option (besides the slick and ugly ones) would be to allow people to submit references from any reference manager, using a standard format (e.g., RIS, BibTeX, etc.). I imagine that would be more complicated, though.
Thanks for giving this feature your consideration, Jon.
Hi,
I'd like to revive this thread since Bookends 10 now provides direct export of references to any refbase online bibliography database. This allows you to share your academic literature with members of your research group or other people in your academic field.
I'm one of the refbase developers and I've enjoyed working with Jon to enable integration with Bookends. As stated in the Bookends release notes, we've setup a public literature database at http://www.refbase.org where everybody is welcome to try out the "Upload to Refbase" feature from within Bookends. The Bookends PDF manual explains this new feature in detail and gives pointers to more information about refbase.
I'm very interested to hear your opinion about this new kind of integration and am very open to improve things further if there's any demand.
To give you a quick example of the current possibilities, Bookends & refbase make it easy for colleagues to collaboratively maintain online bibliographies of their research group or particular topics and authors.
http://sharing.refbase.net/
To do so, refbase allows you to construct URL links to automatically updating bibliographies of particular groups, topics or authors. These links can then be included in your web pages, and users could subscribe to any of your shared bibliographies via RSS feeds.
Here's an example author bibliography:
http://www.refbase.org/show.php?author= ... guchi**%3A
and here's another sample bibliography for a particular research topic:
http://www.refbase.org/show.php?title=T ... cells**%3A
You can easily create similar URLs that point to bibliographies of your institution's research group or that output references directly as Endnote, BibTeX, RTF or PDF. More information is given at:
http://linking.refbase.net/
http://bibliographies.refbase.net/
It's also possible to dynamically include bibliographies such as the ones above into your own web pages. Here's a simple example where a little AJAX-style Javascript fetches results dynamically from refbase.org and injects them into a sample HTML page:
http://www.refbase.org/javascript/include_test.html
More information about this include feature is given at:
http://sourceforge.net/forum/message.php?msg_id=4404553
I hope that the integration of Bookends with refbase will be useful for some of you.
Matthias
--
refbase.net
I'd like to revive this thread since Bookends 10 now provides direct export of references to any refbase online bibliography database. This allows you to share your academic literature with members of your research group or other people in your academic field.
I'm one of the refbase developers and I've enjoyed working with Jon to enable integration with Bookends. As stated in the Bookends release notes, we've setup a public literature database at http://www.refbase.org where everybody is welcome to try out the "Upload to Refbase" feature from within Bookends. The Bookends PDF manual explains this new feature in detail and gives pointers to more information about refbase.
I'm very interested to hear your opinion about this new kind of integration and am very open to improve things further if there's any demand.
To give you a quick example of the current possibilities, Bookends & refbase make it easy for colleagues to collaboratively maintain online bibliographies of their research group or particular topics and authors.
http://sharing.refbase.net/
To do so, refbase allows you to construct URL links to automatically updating bibliographies of particular groups, topics or authors. These links can then be included in your web pages, and users could subscribe to any of your shared bibliographies via RSS feeds.
Here's an example author bibliography:
http://www.refbase.org/show.php?author= ... guchi**%3A
and here's another sample bibliography for a particular research topic:
http://www.refbase.org/show.php?title=T ... cells**%3A
You can easily create similar URLs that point to bibliographies of your institution's research group or that output references directly as Endnote, BibTeX, RTF or PDF. More information is given at:
http://linking.refbase.net/
http://bibliographies.refbase.net/
It's also possible to dynamically include bibliographies such as the ones above into your own web pages. Here's a simple example where a little AJAX-style Javascript fetches results dynamically from refbase.org and injects them into a sample HTML page:
http://www.refbase.org/javascript/include_test.html
More information about this include feature is given at:
http://sourceforge.net/forum/message.php?msg_id=4404553
I hope that the integration of Bookends with refbase will be useful for some of you.
Matthias
--
refbase.net
I'm glad that Jon (and others) are still thinking about this issue. Having skimmed over the Refbase page, and played a tiny bit with the Bookends server feature, I'm not really sure what is possible. So let me give you my ideal scenario and maybe someone can tell me if this is possible with the current versions of Bookends and possibly Refbase. To whatever extent this isn't possible, consider it a feature request.
I'm a member of a lab with 12 people working on various different projects using different OSes and bibliographical software, and we do a lot of literature review for each of these projects. Everybody needs to be able to access everybody else's notes on any text, edit them if needed, add new references, and add/download pdfs.
In my dream world, we would be able to use Bookends as a server for a website we host locally. Any changes made on the website would change the Bookends database, and vice versa. The site would have the ability to manually add data, and also automatic imports for specified formats, so that people who aren't physically in the lab, or who don't have bookends, would be able to use it.
As far as I can tell, this is currently impossible. Am I right? If it was possible, we (and I'm sure many other people) would instantly buy multiple licenses.
The second-best scenario would be to have another web-based solution, like Refbase, and to use Bookends' automatic export to Refbase feature. I guess we could whip up some kind of applescript to automatically send changes in the bookends database to Refbase, using Lingon or something like that, but I suspect the reverse would be quite difficult, no? True syncing would be ideal.
Either way, I would like, as transparently as possible, to be able to use Bookends as my main bibliographical software, but to have a website where other people in the lab could access and edit the same database.
Am I dreaming?
Thanks
I'm a member of a lab with 12 people working on various different projects using different OSes and bibliographical software, and we do a lot of literature review for each of these projects. Everybody needs to be able to access everybody else's notes on any text, edit them if needed, add new references, and add/download pdfs.
In my dream world, we would be able to use Bookends as a server for a website we host locally. Any changes made on the website would change the Bookends database, and vice versa. The site would have the ability to manually add data, and also automatic imports for specified formats, so that people who aren't physically in the lab, or who don't have bookends, would be able to use it.
As far as I can tell, this is currently impossible. Am I right? If it was possible, we (and I'm sure many other people) would instantly buy multiple licenses.
The second-best scenario would be to have another web-based solution, like Refbase, and to use Bookends' automatic export to Refbase feature. I guess we could whip up some kind of applescript to automatically send changes in the bookends database to Refbase, using Lingon or something like that, but I suspect the reverse would be quite difficult, no? True syncing would be ideal.
Either way, I would like, as transparently as possible, to be able to use Bookends as my main bibliographical software, but to have a website where other people in the lab could access and edit the same database.
Am I dreaming?
Thanks
Enkidu, the scenario you are envisioning is exactly why we've started the Bookends<->refbase integration.
I cannot speak for the development plans of the Bookends server and I understand that an all-in-one solution may be the ideal solution. However, this would duplicate a lot of the web functionality that is available in refbase, and this is why we've tried to better integrate Bookends and refbase (instead of re-inventing the wheel).
- upload your references from Bookends (via a direct menu command) or from other reference managers (via export & import)
- manually add references
- upload & download PDFs
- track changes and new record additions via email notifications, RSS feeds or saved queries
- add notes and keywords (public and personal), and setup personal reference groups (these features will be improved in the future)
- automatically import records to -- and fetch/update records from -- the refbase server via a scripted workflow (using the refbase command line clients)
True synching between refbase and Bookends is currently not possible but I'm willing to push this further, if Jon and Bookends users are interested. As mentioned earlier, this is a rather big feature with lots of stuff to be sorted out, so it would surely take some time to implement.
Matthias
I cannot speak for the development plans of the Bookends server and I understand that an all-in-one solution may be the ideal solution. However, this would duplicate a lot of the web functionality that is available in refbase, and this is why we've tried to better integrate Bookends and refbase (instead of re-inventing the wheel).
Please allow me to explain (I really don't want to highjack the forum so forgive me if this is inappropriate). With your user scenario in mind, refbase allows you to:Enkidu wrote:Having skimmed over the Refbase page, and played a tiny bit with the Bookends server feature, I'm not really sure what is possible.
- upload your references from Bookends (via a direct menu command) or from other reference managers (via export & import)
- manually add references
- upload & download PDFs
- track changes and new record additions via email notifications, RSS feeds or saved queries
- add notes and keywords (public and personal), and setup personal reference groups (these features will be improved in the future)
- automatically import records to -- and fetch/update records from -- the refbase server via a scripted workflow (using the refbase command line clients)
True synching between refbase and Bookends is currently not possible but I'm willing to push this further, if Jon and Bookends users are interested. As mentioned earlier, this is a rather big feature with lots of stuff to be sorted out, so it would surely take some time to implement.
Matthias
Thanks for your reply, Matthias.
I had some further thoughts about how Bookends might be able to handle something resembling true syncing with a refbase-based database (or another web solution, for that matter). I apologize if these are totally unrealistic, just trying to get the thoughts out there.
Bookends currently has a manual "export this to refbase" option. What if there was an option to make this automatic, at user-specified time intervals? To make it work, there would have to be some way of knowing (a) the time of the last sync and (b) the time of any changes to the Bookends database. Then in any cases where (b) was after (a), it would be exported. That takes care of one way syncing.
If I understand Matthias correctly, syncing the other way would require Bookends to have RSS capabilities or some kind of saved query. I presume that Refbase keeps track of last updated times for each reference? If so, then you could have the saved query simply ask for any references updated after the time of the last sync. In principle, this isn't be much more difficult than the current capability Bookends has of searching PubMed, is it? RSS feeds might be a bit more work.
As you say, this is a fairly major undertaking, but does the above sound in principle feasible?
Thanks!
I had some further thoughts about how Bookends might be able to handle something resembling true syncing with a refbase-based database (or another web solution, for that matter). I apologize if these are totally unrealistic, just trying to get the thoughts out there.
Bookends currently has a manual "export this to refbase" option. What if there was an option to make this automatic, at user-specified time intervals? To make it work, there would have to be some way of knowing (a) the time of the last sync and (b) the time of any changes to the Bookends database. Then in any cases where (b) was after (a), it would be exported. That takes care of one way syncing.
If I understand Matthias correctly, syncing the other way would require Bookends to have RSS capabilities or some kind of saved query. I presume that Refbase keeps track of last updated times for each reference? If so, then you could have the saved query simply ask for any references updated after the time of the last sync. In principle, this isn't be much more difficult than the current capability Bookends has of searching PubMed, is it? RSS feeds might be a bit more work.
As you say, this is a fairly major undertaking, but does the above sound in principle feasible?
Thanks!
Hi Enkidu, the synchronization process you're describing makes sense to me. In fact, I have just implemented such a modification-date based synchronization feature for the refbase command line client (currently it works with BibTeX or MODS XML files). For each record, refbase stores creation & modification info in the database. Upon export, the upcoming version of refbase will output a string to the notes field that indicates the refbase ID/URL for that reference as well as the date/time when it was last updated. Here's an example record (in BibTeX format):
@Article{Janech++2006IceBindingProteins,
author="Janech, M. G.
and Krell, A.
and Mock, T.
and Kang, J. S.
and Raymond, J. A.",
title="Ice-binding proteins from sea ice diatoms (Bacillariophyceae)",
journal="Journal of Phycology",
year="2006",
publisher="Blackwell Publishing",
address="Oxford",
volume="42",
issue="2",
pages="410--416",
optkeywords="cryoprotection",
optkeywords="diatoms",
optkeywords="sea ice",
abstract="Sea ice diatoms thrive under conditions of low temperature and high salinity...",
optnote="exported from refbase (http://localhost/refs/show.php?record=27274), last updated on Sun, 01 Apr 2007 18:50:09 +0200",
issn="0022-3646",
doi="10.1111/j.1529-8817.2006.00208.x",
opturl="http://www.blackwell-synergy.com/doi/ab ... 06.00208.x",
opturl="http://localhost/files/jphycol/27274_Ja ... inding.pdf"
}
Note the string in the 'optnote' field which indicates the modification info in UNIX time format. A local tool (such as Bookends or the refbase command line client) could now retrieve all unique citation IDs (or refbase serial numbers) from a local bibliography file/database and query the remote refbase server for all records where the modification date on the server is more recent then the local one. In its current implementation, the refbase command line client simply fetches all matching entries from the refbase server and performs the date/time comparison locally. It then updates all local records that were modified on the server since the last synch. In a similar fashion, it is also possible to add records to the local file/database that were added on the server since the last synch.
The described methods currently only work server->local (i.e. not the other way 'round) but that would be possible as well.
I think that something similar could be developed for Bookends, but as mentioned this will require a lot of thought and development time.
@Article{Janech++2006IceBindingProteins,
author="Janech, M. G.
and Krell, A.
and Mock, T.
and Kang, J. S.
and Raymond, J. A.",
title="Ice-binding proteins from sea ice diatoms (Bacillariophyceae)",
journal="Journal of Phycology",
year="2006",
publisher="Blackwell Publishing",
address="Oxford",
volume="42",
issue="2",
pages="410--416",
optkeywords="cryoprotection",
optkeywords="diatoms",
optkeywords="sea ice",
abstract="Sea ice diatoms thrive under conditions of low temperature and high salinity...",
optnote="exported from refbase (http://localhost/refs/show.php?record=27274), last updated on Sun, 01 Apr 2007 18:50:09 +0200",
issn="0022-3646",
doi="10.1111/j.1529-8817.2006.00208.x",
opturl="http://www.blackwell-synergy.com/doi/ab ... 06.00208.x",
opturl="http://localhost/files/jphycol/27274_Ja ... inding.pdf"
}
Note the string in the 'optnote' field which indicates the modification info in UNIX time format. A local tool (such as Bookends or the refbase command line client) could now retrieve all unique citation IDs (or refbase serial numbers) from a local bibliography file/database and query the remote refbase server for all records where the modification date on the server is more recent then the local one. In its current implementation, the refbase command line client simply fetches all matching entries from the refbase server and performs the date/time comparison locally. It then updates all local records that were modified on the server since the last synch. In a similar fashion, it is also possible to add records to the local file/database that were added on the server since the last synch.
The described methods currently only work server->local (i.e. not the other way 'round) but that would be possible as well.
I think that something similar could be developed for Bookends, but as mentioned this will require a lot of thought and development time.
Hi,Enkidu wrote:In my dream world, we would be able to use Bookends as a server for a website we host locally. Any changes made on the website would change the Bookends database, and vice versa. The site would have the ability to manually add data, and also automatic imports for specified formats, so that people who aren't physically in the lab, or who don't have bookends, would be able to use it.
As far as I can tell, this is currently impossible. Am I right?
Bookends Server lets users, on any platform, access Bookends database content. Any changes made in the database would be immediately reflected on the web site (note that databases open on the server can't be accessed, they must be closed). Users can also *add* references to the db in a very flexible manner (for example, if you use PubMed, you could copy the PubMed output (tagged, or MEDLIN format), paste it into a textfield in the browser, and submit it to Bookends for import from the browser.
You cannot edit references via a browser, however.
Jon
Sonny Software