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Old 03-29-2004, 03:50 AM   #1
Samsara
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Post OSS alternative to EndNote?


Hi All!

I'm looking for an open source project that implements reference management features like those found in EndNote.

For what little I know of it, the best features of EndNote are that it imports and exports references in various formats, including BibTeX export (for use with LaTeX; although apparently no LaTeX import); but most of all, that it plugs into MS Word, allowing references to be inserted into word documents and effortless switching between different referencing styles, like author-year vs. numbered. (No, I don't work for them - wait for it!)

The same company have another commercial product, RefViz, which helps to visualise the relationships between different publications. I haven't used that software, but for all I imagine, this must be based on shared author names and overlap in keywords and words in the abstract. I've given my list of relevant publication variables in the appendix below, as far as that goes. From the promo material I've seen, visualisation is in two modes, either as a matrix where values are like correlation coefficients, or a TouchGraph-like web where distances between elements indicate approximate correlation coefficients. The latter mode seems more appealing to me for complex knowledge management, although I can see how they complement each other.

Finally, I noticed that another kind of software that's becoming popular in academic institutions is the mind mapping kind. My university uses MindGenius, although I'm personally partial to The Brain and looking forward to trying version 3. The basic idea is to have a tree or network of related concepts, with links to relevant word documents, pdfs, web sites, html files, powerpoint files etc. for each concept, thus organising thought, source material and one's own contributions.

The way for OSS to conquer academia will be through unifying reference and concept management by implementing a coherent system of features such as those in EndNote, RefViz and MindGenius. For instance, direct links from the reference database GUI to pdf and word files are desirable. I believe the nature of most OSS development (LaTeX GUIs, OpenOffice.org, KOffice and (to a lesser degree) Abiword and Scribus being the most relevant) will facilitate implementation of such a piece of software with interfaces to various other programs.

I wonder whether anyone knows of development of such a clone having begun, and whether anyone would be interested in brainstorming a concept superior to the status quo in the guise of EndNote, RefViz and MindGenius. Finally, if you know of a better place to post a call to arms such as this, let me know!

Many thanks,

Samsara



Appendix:

Possible relevant information about journal papers:
Author(s)
Cited work(s)
Acknowledged persons
Affiliation(s)
Journal
Year
Keywords
words in abstract that could be keywords, considering what keywords are commonly used in that journal (and related journals?)

Could also consider interactions, such as Affiliation-Date (were they actual contemporaries?) and Journal-Date (did they appear in the same issue?)
Might consider correlative relationships between journals, e.g. articles in "Evolution" and "Genetics" more likely related than those in "Genetics" and "Behavioural Ecology".
 
Old 03-29-2004, 03:59 AM   #2
profjohn
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I feel your pain.

I use endnote in WIN, then switch over to Linux and use Open Office. Real bother.

I would certainly be interested in working on something like this. My programming skills are marginal, but I could sure do something.

BTW, I agree that for Linux to really make it in the humanities part of the UNI world, there need to be more projects such as this...

Anyone know if there is another such project already underway?
 
Old 03-29-2004, 09:12 AM   #3
Samsara
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Hmm, yeah, would be nice to get a group together. Problem with this forum is the disproportionate interest devoted to "virgin" posts, by which I mean the ones that have not received a reply.

Like you, profjohn, I have no particular background in application development, although some in programming (mostly Perl, which, again, is not for application development).

But as I said, get a group together and see what we can do. It may end up being a case of defining specifications for the software, raising funding from research institutions that stand to benefit from the end result, and outsourcing the actual coding to more accomplished hackers.

Who else? Raise a hand!
 
Old 03-29-2004, 01:10 PM   #4
Tinkster
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I don't know what to say ... :}


Why would academia (intelligencia) want to
use anything else but LaTeX (with BibTeX,
and probably CVS/RCS) in the first place? :)


If you feel you need to mobilize an army of
programmers go to
comp.text
comp.text.tex
comp.os.linux.development
comp.os.linux.development.apps
comp.programming
comp.os.linux.development.*
.
.
.
and try there ;)



Cheers,
Tink
 
Old 04-01-2004, 01:46 PM   #5
Samsara
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Quote:
Originally posted by Tinkster
Why would academia (intelligencia) want to
use anything else but LaTeX (with BibTeX,
and probably CVS/RCS) in the first place?
I know that computer scientists don't often publish in peer-reviewed journals. I assume you are in that category.

For most other sciences, publishing in peer-reviewed journals is of survival essence. It happens frequently that manuscripts get rejected by the "target" journal. In EndNote, in an ideal case, you'd just reformat your citations in the style required by your second choice journal (should require less than ten mouse clicks; style specification files for hundreds of the most common journals are available), save and resubmit. I'm not aware of such a style library for BibTeX, but I'll admit I've only briefly played with LaTeX/BibTeX so far.

Regards,

Samsara
 
Old 04-01-2004, 02:07 PM   #6
Tinkster
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As a matter of fact I don't publish for my peers,
but have worked in an institution with Physicists,
Biologists and Geologists who did publish, and
they all used LaTeX with BibTeX ...


Cheers,
Tink
 
Old 04-06-2004, 12:00 PM   #7
Samsara
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Hi again Tinkster!

I've thought again about your comments, and it remains absolutely clear in my mind that new ways of visualising knowledge are needed, in the style of RefViz and MindMaps. Mindmaps are a graphical thing, granted, and it may be good to keep this separate from anything that can be textually represented.

The BibTeX format does not support including data on the complex inter-relationships between publications, e.g. what I proposed above, distilled below:

Quote:
visualise the relationships between different publications. I haven't used that software, but for all I imagine, this must be based on shared author names and overlap in keywords and words in the abstract. [...] visualisation is in two modes, either as a matrix where values are like correlation coefficients, or a TouchGraph-like web where distances between elements indicate approximate correlation coefficients. The latter mode seems more appealing to me for complex knowledge management, although I can see how they complement each other.

[...]

Possible relevant information about journal papers:
Author(s), Cited work(s), Acknowledged persons, Affiliation(s), Journal, Year, Keywords

words in abstract that could be keywords, considering what keywords are commonly used in that journal (and related journals?)

Could also consider interactions, such as Affiliation-Date (were they actual contemporaries?) and Journal-Date (did they appear in the same issue?)
Might consider correlative relationships between journals, e.g. articles in "Evolution" and "Genetics" more likely related than those in "Genetics" and "Behavioural Ecology".
I don't know much about Emacs, so if there are Emacs modes that may be helpful achieving what I am trying for, please let me know! Else, I cannot see how the modern needs are addressed by BibTeX and Latex.

Best wishes,

Samsara

Last edited by Samsara; 04-06-2004 at 12:02 PM.
 
Old 04-06-2004, 12:22 PM   #8
tobyj
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1. BibTeX *does* allow you to automatically reformat your references for different journal styles. I have seen many .bst files available for different journals on e.g. personal web sites, journal publisher web sites (e.g. Kluwer are good for this), and a quick (well, 5 minutes)

bash$ tex $(locate makebst.tex)

allows you to make a .bst for any journal style you need.

The natbib package allows you to swap between (Author, date) and numbered references quite easily.

2. I do not think I would want to calculate webs/matrices of connections between the entries in my .bib file. I've read all the papers there and know which ones are interconnected and how. What I need is a tool to find connections in *all the published literature*. The `Related Articles' link on Entrez Pubmed

http://www.ncbi.nlm.nih.gov/PubMed

does this for a subset of the literature relevant to medical science, and using an (unknown to me) algorithm to assess similarity. The ideal tool for me would be accessed over the net, search all (peer reviewed) literature, allow me to specify my own similarity measure, and email me every week to alert me about newly published articles matching specified criteria. Biomail

http://biomail.sourceforge.net/biomail/index.html

does this last thing, allowing only limited types of searches on the Pubmed database though.
 
Old 04-06-2004, 12:38 PM   #9
Samsara
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Quote:
Originally posted by tobyj
What I need is a tool to find connections in *all the published literature*. The `Related Articles' link on Entrez Pubmed

http://www.ncbi.nlm.nih.gov/PubMed

does this for a subset of the literature relevant to medical science, and using an (unknown to me) algorithm to assess similarity. The ideal tool for me would be accessed over the net, search all (peer reviewed) literature, allow me to specify my own similarity measure, and email me every week to alert me about newly published articles matching specified criteria.
Good call!

I absolutely agree with you, and had begun to think along these lines. However, that would require talking to people at e.g. Web of Science and asking them to completely change the way they provide access to their database. I have my doubts as to how responsive one would find those people to be to such new ideas that require *extra work*.

At an application level, it may be possible to do something with Perl modules, e.g. LWP (http://search.cpan.org/~gaas/libwww-....77/lib/LWP.pm), then feed this into Touchgraph through an intermediate similarity-determining algorithm.

Just an idea.

Samsara
 
Old 04-06-2004, 02:32 PM   #10
Tinkster
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Quote:
I've thought again about your comments, and it remains absolutely clear in my mind that new ways of visualising knowledge are needed, in the style of RefViz and MindMaps. Mindmaps are a graphical thing, granted, and it may be good to keep this separate from anything that can be textually represented.
As Yobyi already pointed out, BibTeX DOES support
what you require ... and the rest of what you said is
IMHO just kicking up buzzwords :) ...

modern ... visualisation ...

The fact that you want it graphically and that
your request is new doesn't necesserily mean
that's what everyone wants - and quite frankly,
I don't think that "ease of use" means higher
productivity or better results. Just look at
"haute cusine" and "microwave food" ;}
I rather wait 25 minutes longer for my meal :}
(either cooking myself or going to a nice restaurant)

I've seen secretaries 15 years ago using WordPerfect
DOS, and see them today (ones that have been brought up
with a rodent) ... the ones from the olden days were
more efficient, non-visual and all ;) ... doing
600 WPM as opposed to 200Characters and 50
mouse-clicks per minute.


Cheers,
Tink
 
Old 04-06-2004, 05:00 PM   #11
Samsara
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Tinkster,

I'd be the last person to posit that (text based == inefficient) evaluates as true*. However, some things cannot be done in the orthogonal ascii world. I'm not suggesting that everyone's brains work the same. Perhaps the main benefit of what I'm suggesting is that it would enable one to understand the science community better, which is an integral part of doing science. For instance, tools such as the ones I am proposing may make it easier to follow the name change of an author (e.g. getting married), or find out which institutions they've worked at previously. What I'm saying is, if you can hyperlink it, do so!

Regards,

Samsara


Edit:
* For instance, I use Vim on the console for all text editing, and lynx as my offline browser.

Last edited by Samsara; 04-12-2004 at 03:21 PM.
 
Old 04-26-2004, 08:22 AM   #12
Samsara
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What I propose may turn out to be a reasonably trivial extension to refdb:

http://refdb.sourceforge.net

Samsara
 
Old 05-12-2004, 04:01 PM   #13
dr_bazz
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on line petition for Endnot on Linux

Just "googled" in on this Forum: I was also looking for Endnote versions for Linux. The only reason me and many colleages stick to Windows at work (I try to use Linux as much as I can, though), is that Endnote, a great bibliografy management tool, is not available for Linux. A shame, when they (Endnote) were only aware how much Linux was used in Academics (at least, the sciences), they would get started with their Linux Version right away. I found this on-line petition calling for Endnote on Linux:

http://www.publicmind.com/enduser/group.jsp?node=1083

please enlist all and give the petition your "signature". Hopefully it will work ....

I do not now much about knowledge database software and stuff, sounds interesting though.

Keep the good work going,

dr_bazz
 
Old 05-12-2004, 09:53 PM   #14
clausi
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Quote:
I wonder whether anyone knows of development of such a clone having begun, and whether anyone would be interested in brainstorming a concept superior to the status quo in the guise of EndNote, RefViz and MindGenius.
You may like to test FreeMind.

Concerning bibliographies: Probably every science which uses mathematical formulars on a regular basis, uses the LaTeX/BibTex combination. If you're looking for graphical tools to manage the collection, try pybliographer or JabRef.

Regards.
 
Old 05-14-2004, 03:50 PM   #15
imanish
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Hi,

As suggested earlier, try out refdb (http://refdb.sourceforge.net).

I spent several months searching around for exactly the same thing: an alternative to Endnote. And I finally settled on refdb. It gives you a database server separate from a web or command-line interface (or both). Several users can share references, add annotations of their own, store offprints and do searches. It's support for RIS/Docbook/XSL/BibTeX makes it quite versatile. I've now been using it for more than a year.

The one issue is that it does need some non-trivial setting up initially. It doesn't have a simple RPM installation.

-- manish.
 
  


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