noksagt said: "But EndNote will still get that wrong when it imports them. You can see for yourself by exporting an RIS from EndNote (which will contain attachments) & re-importing it into EndNote (which will put the attachment information into the generic URL column, rather than the file attachment column;"
But you can easily modify the endnote import filter, by goign to edit/import filters/open filter manager and then in the RIS filter go to "templates" and change the L1 field, say from "url" to "link to pdf". This is the practical thing in endnote, that filters are very easy to change.
I have now installed Mendeley to experiment with import/export between Mendeley, Endnote, and Zotero. I can confirm that Mendeley is able to import the following file types: bib, ris, endnote xml, zotero sqlite, pdf. However, Mendeley can only export bib, ris, and endnote xml.
I successfully imported the file zotero.sqlite into Mendeley - the entire 500+ database with attached pdfs - however the unattached pdfs (non-referenced) did not export/import. I have been able to Mendeley/export to Endnote/import with endnote xml but the pdfs do not follow (how surprising). Still the ability to fully export from Zotero to Mendeley does seem to hold some promise for those of us still searching for the Holy Grail of Interoperability.
I have checked migugg's suggestion to rename the field in the RefMan RIS L1 from 'URL' to 'link to pfd' using Endnote's Filter Manager but I was unable to get this to work. The Filter Manager also offers the ability to create a new custom filter but I do not know enough to take on this task. RDF/BIBO possibilities here? By the way, what is 'DIMDI' and could it be used because it appears in EndNotes list of filters.
I did find a link on the Endnote support and services page for Conversion Utilities and wonder if any of these could be tweaked to work with Zotero: http://www.endnote.com/support/enconversion.asp
and
http://www.endnote.com/support/faqs/Import/faq10.asp
I also wonder if these links offer any help
http://www.uns.ethz.ch/pub/publications/xml_format
http://community.muohio.edu/blogs/darcusb/archives/tag/rdf
the former just seems to suggest that endnote xml isn't going to be super helpful, as I don't see a field for a file link there. The latter is concerned with citations in documents and not with porting databases - Bruce is a frequent contributor here and the original author of csl (the citation style language used in Zotero and Mendeley), he is very good in identifying structural issues and thinking longterm - which is what he does in the post you link to. No short-term, and likely not even medium-term solutions there.
I doubt it. At least up to version X, EndNote's import filter could only import tagged or simply delimited files & not SGML/XML-based formats. "EndNote XML import" was, at the time, apparently bolted on & did not use a customizable import facility. While EndNote's filters are customizable, they are extremely limited. Which explains the longstanding lack of even BibTeX import.
By the way, what is 'DIMDI'
Where have you seen this & what leads you to think that it would be useful? The only DIMDI I know of is essentially a database supplier. EndNote does come with filters to allow import of DIMDI resources, as you say. But it is not really much different than Ovid or many other esoteric formats that are also supported. I doubt it has PDF attachment support & it is certainly not a widely utilized format.
"I doubt it. At least up to version X,"
- So what is the possibility of starting with X1 and up, or did you mean all X versions (X2, X3, etc.)?
[By the way, how do you get those neat boxes [ ] around your quotes in this forum?]
"Where have you seen this & what leads you to think that it would be useful? (DIMDI)"
- I found about 20-30 filters with the DIMDI label in the EndNote filter manger, and one of these was listed as "Import DIMDI". It was a long shot and but I was unable to get it to work with pdf thus confirming your hunch that it doesn't support pdf attachments.
I have just been hunting for something (anything) but realize I don't have the technical abilities to guide my search further. I am satisfied that you (the Zotero developers) are aware of this issue and trust that you will publish a workaround if (when) one is found. My feeling is that a third party program like Mendeley, EverNote, Papers (or other software with bib functionality) might hold the key. I'm still waiting for a reply from Endnote but do not have my hopes up given their poor track record on this issue.
What is the next best practice in you view for pdf export: export from Zotero with RIS and then manually link (drag&drop) each pdf into Endnote?
Endnote X and above - I don't think noksagt would know - Endnote pushes out new versions constantly and it's hard to keep up. Most of the time they don't contain major innovations, though ;-)
Citation boxes - select Html below the text box and enclose the quoted text in <blockquote> </blockquote>
btw - I do not believe that Mendeley supports relative links in RIS import - at least I could not find a way to make it work, and any reference on the mendeley site of relative links is in the "desired features" section.
I still think Zotero should put absolute paths to pdfs - both linked and stored - in its RIS output.
Here is my exchange with Endnote (reply just received):
My question:
I use X1 and have a library of nearly 2000 references including 1500 with linked pdfs. However I have colleagues that use other bib man software like Zotero, RefMan, and BibTeX. I'm looking for a way to import/export references together with attached pdfs so we can build one master library. I've been told that the only way to do this is by using one of the open/standard bibliographic exchange formats (RIS,Refer,BibTeX, etc.). Can you please instruct me how to accomplish this?
Their reply:
I cannot tell you how to import or export into or from the other programs, however both EndNote and Reference Manager can import and export RIS files. I believe other programs can also export in this format. You can find the format standard here:
http://www.refman.com/support/risformat_intro.asp. As long as the PDF files are set to absolute links pointing to a location all users can get to, importing the RIS file SHOULD include the PDF links.
So, another point for absolute paths. I hope this helps. If there is any clarification that someone thinks I should ask about please post back here.
Hello, reviving an old post for the sake of absolute paths. I too am trying to ensure that I can move entries between Zotero and Bookends. The developer of Bookends is willing to change his RIS import feature to include the L1 attachment field, but wants to make sure that Zotero can automatically include the necessary absolute path so this works correctly for all users upon exporting out of Zotero.
I have seen in a different thread from 2010 that an alternative RIS translator was made back then that may have allowed for this, but that was 2 years ago, and I am sure the built in RIS translator has undergone change since then. Is it possible to export with an absolute path?
The current solution is that you can export items in RIS with files - that option includes a relative link in L1 and all the exported files in an "files" folder, that seems to me to be a better solution anyway.
There is no current version of the translator with absolute filepaths.
Thank you, Adam. Yes, that is all clear to me, and I have been using it. But the developer of Bookends is clear that he is happy to implement L1 field support to transfer the attachment over, but only *if* some major bibliographic software supports exporting it without end users having to then manually modify the output file. This, in turn, means absolute paths, since relative paths are useless for other pieces of software, it appears.
Would it not be possible to have the absolute path, even if only as an option (like a preference, or checkbox at time of export)?
(p.s. Of course, another way of achieving my goal (being able to transfer files between Zotero and Bookends/other software) is to use Endnote XML -- but I will post on that in the relevant thread.)
why would relative paths be useless to other software? Zotero puts the .ris in a folder together with a files folder containing all attachments it creates - that way, any other program can use/access the same relative path, no modification necessary. (my suspicion is that Bookends devs are confusing this with Endnote, which uses a "relative path" to it's internal pdf directory, that users would need to manually replace for file import to work).
Endnote XML (and any other format for that matter) would have the same issue - absolute paths are a clear second best to relative paths, since they make it impossible to transfer exports between different computers.
edit: leaving this here for future reference - refers to deleted comment above.
T2 is for journal titles as per the official specs. J2 is for "alternate title" and Endnote and Zotero use it for the Journal abbreviation - if there is no journal abbreviation, Zotero will not export anything into J2
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"But EndNote will still get that wrong when it imports them. You can see for yourself by exporting an RIS from EndNote (which will contain attachments) & re-importing it into EndNote (which will put the attachment information into the generic URL column, rather than the file attachment column;"
But you can easily modify the endnote import filter, by goign to edit/import filters/open filter manager and then in the RIS filter go to "templates" and change the L1 field, say from "url" to "link to pdf". This is the practical thing in endnote, that filters are very easy to change.
I successfully imported the file zotero.sqlite into Mendeley - the entire 500+ database with attached pdfs - however the unattached pdfs (non-referenced) did not export/import. I have been able to Mendeley/export to Endnote/import with endnote xml but the pdfs do not follow (how surprising). Still the ability to fully export from Zotero to Mendeley does seem to hold some promise for those of us still searching for the Holy Grail of Interoperability.
I have checked migugg's suggestion to rename the field in the RefMan RIS L1 from 'URL' to 'link to pfd' using Endnote's Filter Manager but I was unable to get this to work. The Filter Manager also offers the ability to create a new custom filter but I do not know enough to take on this task. RDF/BIBO possibilities here? By the way, what is 'DIMDI' and could it be used because it appears in EndNotes list of filters.
I did find a link on the Endnote support and services page for Conversion Utilities and wonder if any of these could be tweaked to work with Zotero: http://www.endnote.com/support/enconversion.asp
and
http://www.endnote.com/support/faqs/Import/faq10.asp
I also wonder if these links offer any help
http://www.uns.ethz.ch/pub/publications/xml_format
http://community.muohio.edu/blogs/darcusb/archives/tag/rdf
The latter is concerned with citations in documents and not with porting databases - Bruce is a frequent contributor here and the original author of csl (the citation style language used in Zotero and Mendeley), he is very good in identifying structural issues and thinking longterm - which is what he does in the post you link to. No short-term, and likely not even medium-term solutions there.
"I doubt it. At least up to version X,"
- So what is the possibility of starting with X1 and up, or did you mean all X versions (X2, X3, etc.)?
[By the way, how do you get those neat boxes [ ] around your quotes in this forum?]
"Where have you seen this & what leads you to think that it would be useful? (DIMDI)"
- I found about 20-30 filters with the DIMDI label in the EndNote filter manger, and one of these was listed as "Import DIMDI". It was a long shot and but I was unable to get it to work with pdf thus confirming your hunch that it doesn't support pdf attachments.
I have just been hunting for something (anything) but realize I don't have the technical abilities to guide my search further. I am satisfied that you (the Zotero developers) are aware of this issue and trust that you will publish a workaround if (when) one is found. My feeling is that a third party program like Mendeley, EverNote, Papers (or other software with bib functionality) might hold the key. I'm still waiting for a reply from Endnote but do not have my hopes up given their poor track record on this issue.
What is the next best practice in you view for pdf export: export from Zotero with RIS and then manually link (drag&drop) each pdf into Endnote?
Cheers!
Citation boxes - select Html below the text box and enclose the quoted text in
<blockquote> </blockquote>
I still think Zotero should put absolute paths to pdfs - both linked and stored - in its RIS output.
My question:
I use X1 and have a library of nearly 2000 references including 1500 with linked pdfs. However I have colleagues that use other bib man software like Zotero, RefMan, and BibTeX. I'm looking for a way to import/export references together with attached pdfs so we can build one master library. I've been told that the only way to do this is by using one of the open/standard bibliographic exchange formats (RIS,Refer,BibTeX, etc.). Can you please instruct me how to accomplish this?
Their reply:
I cannot tell you how to import or export into or from the other programs, however both EndNote and Reference Manager can import and export RIS files. I believe other programs can also export in this format. You can find the format standard here:
http://www.refman.com/support/risformat_intro.asp. As long as the PDF files are set to absolute links pointing to a location all users can get to, importing the RIS file SHOULD include the PDF links.
So, another point for absolute paths. I hope this helps. If there is any clarification that someone thinks I should ask about please post back here.
I have seen in a different thread from 2010 that an alternative RIS translator was made back then that may have allowed for this, but that was 2 years ago, and I am sure the built in RIS translator has undergone change since then. Is it possible to export with an absolute path?
There is no current version of the translator with absolute filepaths.
Would it not be possible to have the absolute path, even if only as an option (like a preference, or checkbox at time of export)?
(p.s. Of course, another way of achieving my goal (being able to transfer files between Zotero and Bookends/other software) is to use Endnote XML -- but I will post on that in the relevant thread.)
Endnote XML (and any other format for that matter) would have the same issue - absolute paths are a clear second best to relative paths, since they make it impossible to transfer exports between different computers.
T2 is for journal titles as per the official specs. J2 is for "alternate title" and Endnote and Zotero use it for the Journal abbreviation - if there is no journal abbreviation, Zotero will not export anything into J2