General help

Integrated bibliography

Integrated bibliography

This is probably a bit obvious but clearly not to me so apologies.

Supposing I was writing pages in a course and wanted to give literature references by including a reference number in the body text and wanted Moodle to append a properly formatted reference, perhaps at the end of the page or as a pop-up, by reading that reference number from the database and writing it out properly formatted. Is this possible now? This would allow efficient reference citing.

I guess I'm talking about something that is a bit End Note-ish

Regards

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Re: Integrated bibliography
Hi Mark,
This is not possible at present in the exact form you ask for. But perhaps there is a better way.

However, Moodle has the power to autolink glossary entries. That means that if a word is used in any Moodle text happens to occur as a glossary entry, e link is automatically created, in such a way that clicking the word opens the glossary explanation for that word in a popup (you may have seen that in action: realize the word "database" in these posts).

If you have bibliography citations in a glossary entered as "Author, Year" then, each time you cite in "Author, year" form the relevant info will be linked. With raw numbers, the system would produce many "false citations" and might become disturbing.

The power of glossaries is that they are not restricted to bibliographic references. You may include a link to to the actual respurce (on line journals, PubMed, Chemical Abstracts, etc.), images (I use Moodle with Jmol and Chime resources), etc. And links to other glossary entries: the power or hyperlinking networks!

- Enrique -

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Re: Integrated bibliography

Hi Enrique

Thanks for the response. What you suggest is a good work-around, although I would rather see the ref link filtered to display more as a bibliographic link

On a second matter, I see you use Jmol. I have written a little filter based heavily upon the mediaplugin filter that replaces links to pdb and mol files with the incantations required for the jmol applet. I wouldn't say it is ready for public issue yet but if you want to have a look me know

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Re: Integrated bibliography

Is it possoble to integrate chime molecules in moodle. I want to teach organic chemistry and since visualations is essential i wanted to incorporate chime and jmol files into my moodle course for my students to be able to rotate the molecules and see them in 3d, Is it possoble?

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Re: Integrated bibliography

James,

There's a fuller discussion of jmol and chime here:

http://moodle.org/mod/forum/discuss.php?d=32561#152236

Basically, chime doesn't like to use files straight from moodle, so you have to keep the data files in a separate folder - see Kathy's contributions on the other forum.

Ewen

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Re: Integrated bibliography - extended question

On a similar note, I am looking to add a biblio module to my course, each reference is a www resource (article or paper) and I have built an excel (xls) speadsheet of essentially metadata. I wondered if it was possible to have a library or Bibilo section as a stand alone - the glossary section dosn't seem to cover it fully. I could then upload my references and meta (author, year, summary, URL, comments etc) in a more organised manner than just the 'add resource' mode. This should theoretically allow for better searching to be undertaken by users..

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Re: Integrated bibliography - Wikindx

HI have you seen WIKINDX3

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Re: Integrated bibliography - Wikindx

I am using it here: starting a collection about Self Determination Theory (SDT) for a user centered e-learning design. I am now looking for theories with alternative explanations - and alternative user centered design guidelines - for this SDT model.  (ELO stands for VLE in Dutch)

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Re: Integrated bibliography - Wikindx

Thanks Ger and Joyce for sharing this. This will help relieve the pressure on my back lugging my computer or books back and forth from the main university library and around the stacks while I look for books or having to take notes on paper and transfer them to the computer later. Not to mention that the more you move a laptop the faster it falls apart. I am going to have this installed on my server and just take my books to one of the computers at the library and enter my notes there and then download it when I get home to Endnote.

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Re: Integrated bibliography - Wikindx

Hi,

I'm curious why you'd want to downgrade your data to Endnote?  If you're specifically looking for something that allows you to take notes etc., store them and search them then WIKINDX is far more powerful than Endnote in what it allows you to store, how much it allows you to store for each resource and how it allows you to search and select those notes.  Also, rather than then having to import your resources from Endnote into some word processor via yet another piece of software such as a plug-in, WIKINDX sports an integrated WYSIWYG word processor that allows you to write a complete article within the one software complete with automatic formatting of citations and bibliographies (the first question here I believe).

Not being a Moodle user myself, a few months back I did post a question here about integrating WIKINDX with Moodle but got no responses so I assume they're happy working independently and side-by-side.

[disclaimer] I'm the main developer for WIKINDX so everything above is probably simply bias against Endnote.[/disclaimer]

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Re: Integrated bibliography - Wikindx

Hi Mark-I've posted something about this at the Wikindx site, but in short, until Wikindx can support Unicode properly, it is of limited use to me. If it can't import or export my Arabic material to or from Endnote, I wouldn't even think of using it as my primary bibliography. I waited years and had to do a lot of workarounds with Endnote until it was Unicode compliant and I am not sacrificing that again.

Besides, I've got a dissertation I've been working on for years with Endnote and Word that I'm nearly finished with, as well as several unfinished articles. I have no intention of converting anything over to another system until I finish those.

However, Wikindx seems to me to have great potential. It would nice if it could be used to write collaborative papers with some sort of tracking interface like a Wiki to keep track of different users' edits. If it had that capability, it would be highly attractive.

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Re: Integrated bibliography - Wikindx

I've posted about this to the SF bug you sent in.

Just in case any else reads this and misunderstands the post above, WIKINDX IS unicode/UTF-8 compliant.  Internally within WIKINDX, everything is stored as UTF-8.   What it doesn't do is encode/decode UTF-8 characters between wikindx <--> Endnote. I had this turned off since I didn't believe Endnote supported unicode but I have since been shown the error of my ways and this functionality will be available in the next release sometime before Christmas.

Writing collaborative papers is the next major development and will be led by the developer of uniwakka -- this has been on the books for several months.

Mark.

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Re: Integrated bibliography - Wikindx

Just to let you know, the CVS version of WIKINDX can now import and export bibliographies to Endnote XML (for v8 and higher) and so properly handles UTF-8 characters from Endnote -> WIKINDX -> Endnote (tested with your Arabic characters).

For your interest, here's the current CHANGELOG:

<<<<<<<<<<<<<<<<<<<<<<<<<<<
v3.3
Focus: Major feature enhancements and minor bug fixes.
FEATURE ENHANCEMENTS:
1/ Improved the parsing for sentences when parsing citations.  WIKINDX language localizers/translators should note some changes to languages/xx/CONSTANTS.php to handle this.  The following input:
"This is not uncommon and, at first sight, this adaptability and flexibility seems admirable, but there is a whole class of computer games (usually of the role-playing epic type such as Neverwinter Nights [cite]277[/cite]) for which Cavalcanti's scathing comments (someone who never worked for Warner Bros.) about cinema music's use of neo-romantic and neo-classical pastiche -- "[i]t is an idiom suited to an atmosphere of "pomp and display". In style, the music of the cinema, by and large, represents a fixation at a stage of development which the art itself left behind about thirty years ago. Tschaikovsky, Rachmaninov, Sibelius, are the spiritual fathers of most cinema music" [cite]250:23[/cite] -- could easily be applied to."
is now correctly converted to (assuming the use of a style such as APA which will split the citation into year and page parts):
"This is not uncommon and, at first sight, this adaptability and flexibility seems admirable, but there is a whole class of computer games (usually of the role-playing epic type such as Neverwinter Nights (Bioware, 2002)) for which Cavalcanti's (1939) scathing comments (someone who never worked for Warner Bros.) about cinema music's use of neo-romantic and neo-classical pastiche -- "[i]t is an idiom suited to an atmosphere of "pomp and display". In style, the music of the cinema, by and large, represents a fixation at a stage of development which the art itself left behind about thirty years ago. Tschaikovsky, Rachmaninov, Sibelius, are the spiritual fathers of most cinema music" (p.23) -- could easily be applied to."
2/ The display of metadata for insertion into the SUWP is similar to the display when searching or selecting metadata:  the resource title is displayed, page numbers are displayed and comments, where appropriate, are displayed with quotes and paraphrases.
3/ Added a further help menu item with tips on using Wikindx.
4/ Improved the ordering of results returned by searching and selecting metadata (now ordered by first creator surname, then publication year and then title and all metadata is ordered by page number).
5/ When displaying a single resource, any metadata now has its keywords displayed and hyperlinked to facilitate selecting other metadata with the same keywords.
6/ Title/subtitle separators are now part of the bibliographic/citation XML style files rather than being a part of the localization system.
7/ Footer or header page numbers can now be added to RTF exports in the word processor.
8/ Select Resources has been improved by allowing a conditional selection across all available fields improving the flexibility and power of the select.
9/ Select Metadata has been improved by allowing a conditional selection across all available fields improving the flexibility and power of the select.
10/ When exporting to RTF from the word processor, users may now define a length of quotation above which the quotation is indented.
11/ Footnotes can be inserted into the word processor.  If the bibliographic/citation style is in-text (for example APA style), these will be displayed as footnotes at the bottom of each page of the RTF export. For bibliographic/citation styles that use footnotes or endnotes for their citations, these footnotes will be either footnotes or endnotes depending on the style.
12/ Added $WIKINDX_SESSION_PATH and$WIKINDX_SESSION_PATH_CLEAR to config.php to give control over where session data is written and how often it is deleted.  This can be a help with wikindices on ISPs where session storage space is subject to a quota.
13/ When exporting a bibliography to bibTeX, the user has the option to map any custom WIKINDX fields to bibtex fields.
14/ Bibliographies can now be exported to Endnote XML files compatible with Endnote v8 and above.  Unlike Endnote Tabbed files, XML files will successfully replicate UTF-8 characters from WIKINDX to Endnote.

BUG FIXES:
1/ A non-admin write user can now paste bibtex resources.
2/ Citations where a style (APA for example) states that the citation is split into year and page parts now find possessive creator names correctly in both RTF and html output.
3/ Corrections to bibliography ordering for SUWP exports.
4/ Backticks are now saved when editing bibliographic templates.
5/ An error messages is now printed if the input file size of attachments exceeds the smallest setting in php.ini.
6/ In bibliography formatting, names following the first in the primary creator list are now formatted correctly.
7/ BibTeX citation keys for BibTeX exports are now generated in a consistent manner.
8/ Backslashes are no properly handled in resource input and editing.
9/ When inputting or editing creator names, the requirement now is that initials be entered in the form 'M.N.' or 'Th.V.'.  This means that UTF-8 characters and initials such as 'Th.' are now properly stored.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

This will be released soon as v3.3.

Mark.

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Wikindx - integration with Moodle?
Mark - two questions:

1. Is there a way of allowing a user already logged into a Moodle site to be seamlessly logged in to a wikindx? As I understand it, users have to log in to Wikindx so they would have to log on to Moodle separately (and vice versa).

2. (Sort of related...) Would it be possible to stop people going straight to Wikindx if it's on a moodle installation - so that it is more integral to Moodle. I was thinking more of a Moodle module. The only way I can integrate Wikindx into my Moodle at the moment is use a 'Link to a file or website resource' which means that the whole template is carried through - which duplicates my Moodle theme because I need the branding if you view it as a standalone Wikindx.

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Re: Wikindx - integration with Moodle?

Hi Jon,

Sorry, just come cross this your post.

1/ Not currently.  It would need some writing of cookies granting access to both systems (I'm assuming moodle uses cookies).  Or, the wikindx authorization would need modifying to look for a moodle cookie and of course the username/password combination would need to exist in wikindx's database.

2/ I suggested wikindx as a moodle module on this forum about ayear ago but got no response.  Not knowing moodle, I wouldn't be able to do this myself but would welcome someone working on it as I think the two programs are highly complementary.

Mark.

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Re: Wikindx - integration with Moodle?

I'm not a programmer but I would be very interested in helping out in any way I could in getting this integrated into Moodle.

Mark-Do you know of anyone or any institution that uses both Wikindx and Moodle? Perhaps approaching them to fund such a project would get the ball rolling.

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Re: Wikindx - integration with Moodle?

I've just spotted this thread. Wikindx looks interesting. I've created a basic "Wikindx filter" for Moodle which allows you to cross-link to a wikindx entry by typing (for example) wikindx:646

The filter is in contrib CVS, named "filter_wikindx".

Maybe this can be a seed for someone else to take it further...

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Re: Wikindx - integration with Moodle?

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Re: Wikindx - integration with Moodle?

Hi Dan - this is very good, thanks.

I'm with Nicole on this one - I'm very keen to see this excellent resource incorporated into Moodle. I'm not a developer either, but maybe we could draw up a specification for the developers to work on - it might help focus out thoughts so that we could present a 'business case' in terms of potential funding streams as well. I don't mind drafting something up as a starting point. (Edit - see http://docs.moodle.org/en/wikindx)

Helen, your Royal Stewardness , does this discussion need moving to another Forum?

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Re: Wikindx - integration with Moodle?

I'm very glad to see someone taking this on board.  Although I don't use Moodle myself, I'm happy to help in any way I can.  I've added some thoughts to the wiki.

Mark Grimshaw.

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Re: Wikindx - integration with Moodle?
Good work Dan.

Jon, as you suggest, I'm moving this discussion to a more appropriate forum...

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Re: Wikindx - integration with Moodle?

No-one willing to take up the gauntlet then?

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Re: Wikindx - integration with Moodle?

I'd suggest you be in touch with Janne. If it is going to be integrated, it will most likely need to be integrated at some level through the html editor and he might be able to make a suggestion on how to do this.

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Re: Wikindx - integration with Moodle?

Who is Janne and how do I get in touch with him/her?

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Re: Wikindx - integration with Moodle?

Janne Mikkonen
He's the one with the big head in the picture, not the small one!

He's the person responsible for the html editor. As per our discussion elsewhere, I think adding Wikindx to Moodle would be most useful if it were integrated with the editor. And he's the person who would best know how to do that. As I said, he helped me to integrate a hieroglyphic editor in my site which involves opening up a popup, typing some code, previewing the rendered output in the popup, and then clicking on a button and having the html inserted back into the editor. It's the same process with many of the other features of the editor, like inserting images, etc. In fact, you might want to take a look yourself at the code for inserting images as it might give you some idea how to integrate Wikindx.

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Re: Wikindx - integration with Moodle?
I can't help much with this sorry (too much on my list already, and we do already have a Database module that can be used for applications like this) but it'd be nice to see someone else attempt it.

Probably the best idea would be to integrate it as a new activity module, though this would take some work.

First there probably needs to be more discussion and mock screenshots about how the ideal interface for this should work and where the integration points are exactly.

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Re: Wikindx - integration with Moodle?

Martin-I don't think the database module would work for this. First of all, because you can't rely on a single template to format the references-a book, a journal article, a newspaper article, etc. all have different formatting rules, and these rules differ within a reference type depending on the presence or absence of some piece of information, e.g. if a book has a translator or not you need to insert an "edited by" into the reference. But even if these problems could be overcome with the database module, it still would limit you to producing bibliographies.

Which brings me to the second point, it would be nice to be able to output a footnote or reference anywhere within Moodle. If I want to write something and cite Dougiamas 2002, if this were made available as a plugin, it would allow for that.

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Re: Wikindx - integration with Moodle?

Agree with your points N.

"it would be nice to be able to output a footnote or reference anywhere within Moodle"

Yes, absolutely. My very simple beginning at a wikindx filter was towards that aim - type "wikindx:355" wherever you want and it becomes a link to the wikindx entry. Someone else should improve it so that it also makes it "look" like a standard footnote/reference, by taking the biblio info from wikindx.

I created the basic filter so others would have a base to work from. Please, developers, feel free to completely rework it, hack it to bits, improve it! I'm moving on from my current job and certainly won't have time to work on it.

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Re: Wikindx - integration with Moodle?

I also don't think the buzz database module accomplishes the request here.  If I can summarize the request, it's to have a properly and automatically cited reference within a block of text.  The suggestion is to have wikindx working alongside moodle for this and to use the wikindx database entries and its citation formatting to accomplish this.  Presumably, properly formatted references inserted by teachers are a spur to students to reference correctly themselves so would be a good thing in the moodle context (teaching by example).

I have enough work with wikindx and my PhD and am not familiar with moodle development so, yes, someone else is required for this although I'm happy to program whatever is required on the wikindx side.

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Re: Wikindx - integration with Moodle?

Mark-I just posted this as a project suggestion here.

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Re: Wikindx - integration with Moodle?

Thanks.  I hope we ensnare someone.

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Re: Wikindx - integration with Moodle?

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Re: Wikindx - integration with Moodle?

Good work -- thanks.

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Re: Wikindx - integration with Moodle?

Hi all,

Haven't been back here for some time. Just to let you know that the impending v3.7 wikindx will be able to integrate with CMSs like moodle. I have it working with phpwcms using that system's replacement tags.

List of wikindx resources (by various parameters) can be displayed and a block of text containing wikindx references can be sent to wikindx for citation formatting and extraction of bibliography (and footnotes if that's the citation style).

All the CMS needs to do is to be able to handle replacement tags and to use file_get_contents(URL) or similar using CURL. WIKINDX simply provides the hooks for you to grab the data.

I'm hoping it will be released in a week's time.

Mark.

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Re: Wikindx - integration with Moodle?

Hello

I also run a moodle site which teaches arabic.

I would like to know if theres any progress towards creating a resource to be used with Moodle which allows Wikidx integration.

Has anyone come close to it ?

Does anyone else uses moodle to teach Arabic ?

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Re: Wikindx - integration with Moodle?

Hi,

I think Geoffrey Rowland is working on this. See:

http://moodle.org/mod/forum/discuss.php?d=76936

Mark

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Re: Wikindx - integration with Moodle?

Yes...

Should have something in the next day or so! just tidying a few details up.

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Re: Wikindx - integration with Moodle?

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Re: Wikindx - integration with Moodle?

Sorry, I don't know of any institutions using both moodle and wikindx.

[plug]WIKINDX v3.4 released yesterday.[/plug]

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Re: Integrated bibliography - Wikindx - Endnote

You can integrate with Endnote...
Endnote Tabbed Files:
Use this to create a tabbed file suitable for importing into Endnote. Once you have produced a bibliographic list through the use of 'list', 'select' or 'search' functions, you can then create an Endnote tabbed file.

Select 'Export Endnote' from the 'File' menu to create and download your Endnote file.

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