I am surprised that there is only one request for this. I am struggling with this same issue.
I have one specific problem when using Zotero for a specific purpose. I am working with a couple of medical students to use Zotero for their ePortfolios. We have a home-grown ePortfolio system where all medical students get narrative formative and summative feedback through out their 5 years. These assessments are competency based (similar to ACGME competencies) and organized into areas of improvement and areas of strength. These are all done online and when submitted, they appear in the students' ePortfolio workspaces. The students write essays (ePortfolios) regarding their meeting various standards in each competency citing the evidence from the assessments.
We use EndNote or RefWorks to allow students to download all their references (assessment information), write their essays, cite the references, and then upload it all into a review area. The citations work as hyperlinks so when reviewer reading the essay wants to look at one of the cited references s/he has to just click on the citation to open a new window where the assessment form is displayed.
The problem I am facing with Zotero is that we cannot figure out how to make the citations in the text of the essay or in the bibliography clickable without going to each one and editing them. Since some of the students have as many as a 100 references in their bibliography this is not a viable solution.
It is very surprising that though Zotero is built on the philosophy of getting the references from online databases, it seems to have neglected the fact that the manuscripts written by people using Zotero would be reviewed online where it would be critical for these citations to be hyperlinks!
I am relatively new to Zotero and am quite possibly missing something. I have scoured the Zotero forums, Googled the web and found nothing so far. Maybe the CSL does not at present allow this to occur? Would it be possible to add a "Web style" to Zotero's growing list of styles? If someone can do that, it will be the most appreciated!
This has nothing to do with CSL; it's an implementation issue (and I'd say bug).
I would say that Zotero should be wrapping all URLs variables in HTML links. Further, they should create hyperlinked version of identifiers that have obvious web mappings (like, say, DOIs).
And as I keep saying, I'd like to see RDFa support. I really don't like what i see ATM with the HTML getting output from the server; it's not as well structured as it should be, and I'm not sure it reflects a very clear idea of how to model these data.
In reference to the comment by bdarcus above... So I should not waste my time to try and find a solution for this? we just have to wait till Zotero developers can get around to fixing this? If that is true, then we probably will stick to EndNote/Refworks for now. Thanks for any advice anyone can give regarding this.
You're going to have to wait on Dan Stillman for an answer on Zotero fixes and such, but I'd like to ask while I'm here (since Dan may well wonder the same thing), when you say ...
The problem I am facing with Zotero is that we cannot figure out how to make the citations in the text of the essay or in the bibliography clickable without going to each one and editing them. Since some of the students have as many as a 100 references in their bibliography this is not a viable solution.
... what links are pointing where? Do you mean, for example, that you have in-text author-date citations that you want to link to their respective bibliographic entries, and from there to the original source?
I put in a quick hack on the trunk to wrap URLs and DOIs in HTML links. It's not very sophisticated, nor is it the right place in the code to do it, but it should do the trick until the new CSL processor, which should do this correctly, is ready. Let me know if you find any problems with the pattern matching.
Also, this only applies to HTML bibliographies, not word processor documents.
Dan, Thanks for the response. Am truly impressed with the support provided. I will try this out Monday and let you know.
Bdarcus, I would like to have numbered in text citations which would be hyperlinked to the web page. The bibliography would be author, date, URL with the URL being a hyperlink to the web page. Thanks again!
Dan, thanks again. Is there any hope for the Word Add on in the near future? We are having the students create an essay with citations and bibliography in Word with the word add on; then save as .mht and upload to their ePortfolio. Our reviewers are just reading their essays online and since they all use IE the .mht is not a problem.
We created a patch that looks at the uploaded essay --> scans the bibliography and parses it --> and picks up the URLs --> and then converts each numbered citation to a hyperlink to their evidence. We are piloting this with the students. If this works then we will not need the Word Add on to create hyperlinks. But this process is dependent on students creating a bibliography after they have inserted all the citations. If the citation is not in the bibliography, the process breaks down. Also they have 2 citations next to each other e.g. (1,2) and they manually delete the comma this breaks down. So we are close to having a bandaid but would love to have this built into the Add on itself! I am sure others would like this feature too!
We are having the students create an essay with citations and bibliography in Word with the word add on; then save as .mht and upload to their ePortfolio. Our reviewers are just reading their essays online and since they all use IE the .mht is not a problem.
This issue intersects with a number of things I've been thinking about, with ePortfolios and LMSs being one of them (a hint of the long story is here; ePortfolios were part of this whole discussion).
So your approach is to have students write in a single, proprietary, word processor, save that to a proprietary file format, which then gets uploaded as a dumb file (e.g. a link), which can only be read by another proprietary application, which only runs on a single, proprietary, OS.
I'm not picking on you, but this seems insane. Is there not a better way?
What do your reviewers need to be able to review these documents? Why, for example, can't they just view HTML?
You could then run tidy on the HTML exported from Word to clean up (say, with this option), and you'd have a relatively clean HTML document that could be read by anyone, directly from within any browser.
That would seem from my naive perspective to be a better, more generic, approach to publishing Zotero-enhanced document to the web. Is there something that doesn't make it feasible?
Bruce, I appreciate your comments. I think what I have not stated before is the environment is a medical college where most reviewers are "busy" clinicians or basic science researchers. Their level of computer expertise is very variable. For example, it was a huge jump for some of them to review an essay online rather than on paper. Some needed training to handle >1 open window. Having gotten them comfortable with the exact steps to do the reviews, it is would be a daunting task to change it all and retrain them.
Reviewing the ePorfolio is a very high stakes task. There is a risk (hopefully a small one) of their experience with the technology impacting how they assess the essay. So we have tread gently. The reviewers work at different locations, some using locked down computers which have IE 6.0 as the only browser. For most of them, the technology that is used is the least of their concerns, it is the user experience - what matters is - they don't need to download anything, they don't need to learn something new, they can call the Help desk for support for an application and get intelligent help... You get the idea. Sometimes one has to design for the lowest common denominator.
Having said that we are always looking for a way to make the process easier - thus piloting using Zotero for students. Clearly there are advantages and we might adopt this as long as the process stays unchanged or even improved for the reviewers.
This is reality. You can have the best technology, something that is cheaper, easier, better, but will have a hard time getting it adopted. Nancy Lorezi (current AMIA president) wrote a terrific paper almost 10 years back. Makes for great reading. http://www.jamia.org/cgi/content/abstract/7/2/116
I understand all that, but was just wondering why don't you have the students do "Save As: Web Page, Filtered"? What usability advantage does .mht have over HTML, either for your students, or your reviewers?
Since you're already doing some scripting on the output file to reconstruct the links, am just pointing out that running tidy on it is a trivial thing. And given that this is a good, generic, approach, it can be used more widely.
Part of me gets offended, frankly, when administrators and such tout usability as the reason for a technology decision, but in choosing a particular proprietary solution, they exclude me from using it (because I use a Mac, or LInux, etc.). I am NOT aiming this critique at you personally (indeed, this is partly some issues at my institution); just saying.
Bruce, but there are nifty mht addons for FF, which I just discovered after I look with some puzzlement at a file I got, so this isn't actually excluding anyone (and as you know I run linux, too).
That said, I agree, nothing that mehtan describes seem to make use of .mht's distinctive features.
Adam, Bruce, This must be getting to be the longest thread in Zotero! Remember the users in most cases here do not want to use FF or Safari or Opera. They are happy with the browser that they have that they figured out how to use (actually some have not - they still don't type in URLs - they just follow hyperlinks to get where they need to go). The would not know a Tab if it was served to them on a silver platter with watercress around it. They are NOT excited about technology as we might be. They do not want to download anything (e.g. Tidy) - it is a lot easier for them to do File>> save as >> *.mht. They do not care about the junk that WORD adds to the file. So if we ask them to go through some extra steps - it has to be so they see a tangible benefit. They would not see any benefit from using Tidy. These are very bright people in their own fields but they would much rather hire someone to set up their new computer then do it themselves. Zotero exites them becuase of the tags, snapshots, annotation/notes, search etc. This is why they would go through the effort to change. Hope that makes sense.
If I understand Bruce correctly he just suggests using html instead of .mht.
The tidy could be run by you centrally rather than the users. And the problem with .mht is that users that - for whatever reason - are accustomed to Safari or FF, but otherwise conform to the usage patterns described by you wil not know what to do with an .mht file.
Yes, I misunderstood a bit. mehtan1 mention a "patch" rather than a post-script (which I was assuming).
But leave aside tidy; doing a simple "Save As: Web Page, Filtered" from Word achieves more-or-less the same. That's the same process as "Save As: MHT"; no "additional steps."
And ditto what adamsmith is saying; your users this time around may well all be happily using IE. But I don't think you want to assume that, since if you have one person that prefers Safari or FF, it will be a MAJOR usability problem for them to be confronted with MHT.
We changed from EndNote to Refworks because of the web functionality (access to your library from any online computer) about 4 years back. Refworks also has a Word Add on. When those WORD documents with citations and bibliographies were saved as HTML we variably got errors with the uploaded files. When saved as .mht these went away. These were I believe user errors when creating the citation/bibliographies, but I can't recall for sure right now.
We were busy with some other projects but are now circling back to our ePortfolio application and looking at Zotero, etc. So will explore "tidying" up the files as part of this process.
Enjoyed this discussion and thanks for the advice!
Yes. We need to publish bibliographies online (HTML export from Zotero & copy-paste into a webpage). Not only does it help us because it's quick and easy, it also makes our webpage Zotero-compatible (which is good as we teach Zotero - and no other - to our students).
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I have one specific problem when using Zotero for a specific purpose. I am working with a couple of medical students to use Zotero for their ePortfolios. We have a home-grown ePortfolio system where all medical students get narrative formative and summative feedback through out their 5 years. These assessments are competency based (similar to ACGME competencies) and organized into areas of improvement and areas of strength. These are all done online and when submitted, they appear in the students' ePortfolio workspaces. The students write essays (ePortfolios) regarding their meeting various standards in each competency citing the evidence from the assessments.
We use EndNote or RefWorks to allow students to download all their references (assessment information), write their essays, cite the references, and then upload it all into a review area. The citations work as hyperlinks so when reviewer reading the essay wants to look at one of the cited references s/he has to just click on the citation to open a new window where the assessment form is displayed.
The problem I am facing with Zotero is that we cannot figure out how to make the citations in the text of the essay or in the bibliography clickable without going to each one and editing them. Since some of the students have as many as a 100 references in their bibliography this is not a viable solution.
It is very surprising that though Zotero is built on the philosophy of getting the references from online databases, it seems to have neglected the fact that the manuscripts written by people using Zotero would be reviewed online where it would be critical for these citations to be hyperlinks!
I am relatively new to Zotero and am quite possibly missing something. I have scoured the Zotero forums, Googled the web and found nothing so far. Maybe the CSL does not at present allow this to occur? Would it be possible to add a "Web style" to Zotero's growing list of styles? If someone can do that, it will be the most appreciated!
I would say that Zotero should be wrapping all URLs variables in HTML links. Further, they should create hyperlinked version of identifiers that have obvious web mappings (like, say, DOIs).
And as I keep saying, I'd like to see RDFa support. I really don't like what i see ATM with the HTML getting output from the server; it's not as well structured as it should be, and I'm not sure it reflects a very clear idea of how to model these data.
So I should not waste my time to try and find a solution for this? we just have to wait till Zotero developers can get around to fixing this?
If that is true, then we probably will stick to EndNote/Refworks for now.
Thanks for any advice anyone can give regarding this.
Also, this only applies to HTML bibliographies, not word processor documents.
Thanks for the response. Am truly impressed with the support provided. I will try this out Monday and let you know.
Bdarcus,
I would like to have numbered in text citations which would be hyperlinked to the web page.
The bibliography would be author, date, URL with the URL being a hyperlink to the web page.
Thanks again!
For example with the following link
http://www.ncbi.nlm.nih.gov/pubmed/12693567
only the part up to nih got hyperlinked and the link pointed to http://www.ncbi.nlm.nih
with some others worked.
I need to get it to work with the Word Add on...
The Word plugin doesn't use HTML, so that's a separate issue.
thanks again.
Is there any hope for the Word Add on in the near future?
We are having the students create an essay with citations and bibliography in Word with the word add on; then save as .mht and upload to their ePortfolio. Our reviewers are just reading their essays online and since they all use IE the .mht is not a problem.
We created a patch that looks at the uploaded essay --> scans the bibliography and parses it --> and picks up the URLs --> and then converts each numbered citation to a hyperlink to their evidence. We are piloting this with the students. If this works then we will not need the Word Add on to create hyperlinks. But this process is dependent on students creating a bibliography after they have inserted all the citations. If the citation is not in the bibliography, the process breaks down. Also they have 2 citations next to each other e.g. (1,2) and they manually delete the comma this breaks down. So we are close to having a bandaid but would love to have this built into the Add on itself! I am sure others would like this feature too!
So your approach is to have students write in a single, proprietary, word processor, save that to a proprietary file format, which then gets uploaded as a dumb file (e.g. a link), which can only be read by another proprietary application, which only runs on a single, proprietary, OS.
I'm not picking on you, but this seems insane. Is there not a better way?
What do your reviewers need to be able to review these documents? Why, for example, can't they just view HTML?
You could then run tidy on the HTML exported from Word to clean up (say, with this option), and you'd have a relatively clean HTML document that could be read by anyone, directly from within any browser.
That would seem from my naive perspective to be a better, more generic, approach to publishing Zotero-enhanced document to the web. Is there something that doesn't make it feasible?
I appreciate your comments. I think what I have not stated before is the environment is a medical college where most reviewers are "busy" clinicians or basic science researchers. Their level of computer expertise is very variable.
For example, it was a huge jump for some of them to review an essay online rather than on paper. Some needed training to handle >1 open window. Having gotten them comfortable with the exact steps to do the reviews, it is would be a daunting task to change it all and retrain them.
Reviewing the ePorfolio is a very high stakes task. There is a risk (hopefully a small one) of their experience with the technology impacting how they assess the essay. So we have tread gently. The reviewers work at different locations, some using locked down computers which have IE 6.0 as the only browser. For most of them, the technology that is used is the least of their concerns, it is the user experience - what matters is - they don't need to download anything, they don't need to learn something new, they can call the Help desk for support for an application and get intelligent help...
You get the idea. Sometimes one has to design for the lowest common denominator.
Having said that we are always looking for a way to make the process easier - thus piloting using Zotero for students. Clearly there are advantages and we might adopt this as long as the process stays unchanged or even improved for the reviewers.
This is reality. You can have the best technology, something that is cheaper, easier, better, but will have a hard time getting it adopted. Nancy Lorezi (current AMIA president) wrote a terrific paper almost 10 years back. Makes for great reading. http://www.jamia.org/cgi/content/abstract/7/2/116
Since you're already doing some scripting on the output file to reconstruct the links, am just pointing out that running tidy on it is a trivial thing. And given that this is a good, generic, approach, it can be used more widely.
Part of me gets offended, frankly, when administrators and such tout usability as the reason for a technology decision, but in choosing a particular proprietary solution, they exclude me from using it (because I use a Mac, or LInux, etc.). I am NOT aiming this critique at you personally (indeed, this is partly some issues at my institution); just saying.
That said, I agree, nothing that mehtan describes seem to make use of .mht's distinctive features.
This must be getting to be the longest thread in Zotero!
Remember the users in most cases here do not want to use FF or Safari or Opera. They are happy with the browser that they have that they figured out how to use (actually some have not - they still don't type in URLs - they just follow hyperlinks to get where they need to go). The would not know a Tab if it was served to them on a silver platter with watercress around it. They are NOT excited about technology as we might be. They do not want to download anything (e.g. Tidy) - it is a lot easier for them to do File>> save as >> *.mht.
They do not care about the junk that WORD adds to the file. So if we ask them to go through some extra steps - it has to be so they see a tangible benefit. They would not see any benefit from using Tidy. These are very bright people in their own fields but they would much rather hire someone to set up their new computer then do it themselves.
Zotero exites them becuase of the tags, snapshots, annotation/notes, search etc. This is why they would go through the effort to change.
Hope that makes sense.
The tidy could be run by you centrally rather than the users. And the problem with .mht is that users that - for whatever reason - are accustomed to Safari or FF, but otherwise conform to the usage patterns described by you wil not know what to do with an .mht file.
But leave aside tidy; doing a simple "Save As: Web Page, Filtered" from Word achieves more-or-less the same. That's the same process as "Save As: MHT"; no "additional steps."
And ditto what adamsmith is saying; your users this time around may well all be happily using IE. But I don't think you want to assume that, since if you have one person that prefers Safari or FF, it will be a MAJOR usability problem for them to be confronted with MHT.
We changed from EndNote to Refworks because of the web functionality (access to your library from any online computer) about 4 years back. Refworks also has a Word Add on. When those WORD documents with citations and bibliographies were saved as HTML we variably got errors with the uploaded files. When saved as .mht these went away. These were I believe user errors when creating the citation/bibliographies, but I can't recall for sure right now.
We were busy with some other projects but are now circling back to our ePortfolio application and looking at Zotero, etc. So will explore "tidying" up the files as part of this process.
Enjoyed this discussion and thanks for the advice!
Sorry to reactivate an old question. I face the same problem described above:
url are not active in my bibliographies.
I saw Dan's quick hack, but I don't know if it still works and where to put that?
Where and how can I fix that?
Raphaël
We need to publish bibliographies online (HTML export from Zotero & copy-paste into a webpage).
Not only does it help us because it's quick and easy, it also makes our webpage Zotero-compatible (which is good as we teach Zotero - and no other - to our students).