Annotum Alpha Released
Carl Leubsdorf, Jr.
--
_______________________
Carl Leubsdorf, Jr.
Solvitor ► Problem Solved.
+1 240 389 2255
ca...@solvitor.com
Skype: carlthewebmaster
Mark Hahnel
This looks fantastic. I couldnt find a demo so I set one up here: http://collabbook.org/
It looks really good for an alpha, at the moment Im a bit confused as to how to display a list of the articles.
For anyone else who wants to test it out, sign up on the demo site and we'll play around with the review funtion etc.
Cheers,
Mark
Martin Fenner
Best,
Martin
Am 24.06.11 00:50 schrieb "Mark Hahnel" unter <mha...@imperial.ac.uk>:
Dubi Kanengisser
Carl Leubsdorf, Jr.
Carl Leubsdorf, Jr.
Dubi Kanengisser
Dubi Kanengisser
Carl Leubsdorf, Jr.
Carl Leubsdorf, Jr.
phpinfo();
?>
Carl Leubsdorf, Jr.
Dubi Kanengisser
Dubi Kanengisser
Carl Leubsdorf, Jr.
Dubi Kanengisser
Dubi Kanengisser
Martin Fenner
I’ve also set up Annotum and used Phil Bourne’s example PLoS Comp Biol article from the Beyond the PDF workshop:
http://blogs.xartrials.org/annotum/article/the-mycobacterium-tuberculosis-drugome-and-its-polypharmacological-implications/
Annotum looks nice, and the coauthors part seems to work well. Two quick comments:
- Wordpress sometimes get a little bit confused, as it expects posts and not articles (e.g. In the Dashboard)
- You can add Post Authors, Coauthors and an author in three different places, which is confusing
- The author template doesn’t seem to display the articles of that author or his biographical information
Further testing will tell how well Annotum plays with the scholarly plugins out there. My ePub Export plugin currently only works with posts and pages. It should be easy to make it work with Annotum – ideally with an ePub button next to the “PDF” and “XML” export buttons.
Best,
Martin
Am 25.06.11 03:01 schrieb "Carl Leubsdorf, Jr." unter <ca...@solvitor.com>:
Mark Hahnel
Thanks,
Mark
Mark Hahnel
Martin Fenner
- Install version 1.1.1 of my ePub Export Plugin (released today, adds support for article custom post type)
- Make small changes to two Annotum files (tools-bar.php and template.php): https://gist.github.com/1046450
Kaveh Bazargan
[...]
> You can see this in action
> here: http://blogs.xartrials.org/annotum/article/the-mycobacterium-tuberculosis-drugome-and-its-polypharmacological-implications
Why are your figures in Doc format, Martin? ;-)
--
Kaveh Bazargan
www.river-valley.com | www.river-valley.tv | www.bazargan.org
Dubi Kanengisser
http://dubikan.com/journal/ .
I've been toying around with it a bit, and I've encountered something
odd - the post on the front page doesn't display links in it. The link
is there if you open the post on its own... I can't figure this out.
Any ideas?
Dubi
On Jun 24, 10:00 pm, "Carl Leubsdorf, Jr." <c...@solvitor.com> wrote:
> Sorry about that!! The amazing thing is that hosts are still using 4.x when
> 5.x came out in 2004! Bad on us though for not either informing you or
> coding for 4.x+5.x.
>
> FWIW, Sourceforge.net allows essentially free hosting and could be used to
> host a test site.
>
>
>
>
>
>
>
>
>
> On Fri, Jun 24, 2011 at 9:46 PM, Dubi Kanengisser <dubi...@gmail.com> wrote:
> > Yeah, it's 4.4.9. So that means I can't use annotum unless I get my
> > provider to upgrade? Bummer... Oh well...
>
> > Dubi Kanengisser
>
>
> >> A quick search on that error message turns up:
> >> <<
> >> The private and public keywords for access control are features from PHP
> >> 5. Likewise, the constructor declaration __construct() is a PHP 5 feature.
>
> >> Are you running PHP 4.x? You can always check by sticking a test.php file
> >> in your root that contains just:
> >> <?php
>
> >> phpinfo();
>
> >> ?>
>
> --
> _______________________
> Carl Leubsdorf, Jr.
> Solvitor ► Problem Solved.
> +1 240 389 2255
> Skype: carlthewebmaster
Carl Leubsdorf, Jr.
post, a default for that kind of content. You can change the home page
to be a static 'page' rather than a list of recent posts via the
dashboard > settings > reading.
Hope this helps.
-C
_____________________
Carl Leubsdorf, Jr.
Dubi Kanengisser
Dubi Kanengisser
Carl Leubsdorf, Jr.
Dubi Kanengisser
Dubi Kanengisser
Martin Fenner
- talk directly to CrossRef and PubMed (the Kcite plugin, http://wordpress.org/extend/plugins/kcite/)
- use the WordPress Links Manager (my Wordpress Link to Link plugin, http://wordpress.org/extend/plugins/link-to-link/)
- Embed reference information directly in HTML, using a standard format ( Scholarly HTML, http://ptsefton.com/2009/04/07/scholarly-html-simple-rational-modern-citations-using-links.htm)
These three approaches can of course be combined.
Martin
Am 25.06.11 21:14 schrieb "Dubi Kanengisser" unter <dub...@gmail.com>:
>> +1 240 389 2255 <tel:%2B1%20240%20389%202255>
>> c...@solvitor.com
>> Skype: carlthewebmaster
Phillip Lord
This looks interesting. How separable is the review workflow system? We
have been using EditFlow, which works but doesn't quite fit perfectly
(actually it has too much stuff that just confuses).
"Carl Leubsdorf, Jr." <ca...@solvitor.com> writes:
> Today I'm pleased to announce the alpha release of Annotum, the scholarly
> authoring and publishing platform based on WordPress.
>
> http://wp.me/p1syru-1Q for more info and information on how to get started.
>
> Comments/questions welcome!
>
> -C
--
Phillip Lord, Phone: +44 (0) 191 222 7827
Lecturer in Bioinformatics, Email: philli...@newcastle.ac.uk
School of Computing Science, http://homepages.cs.ncl.ac.uk/phillip.lord
Room 914 Claremont Tower, skype: russet_apples
Newcastle University, msn: m...@russet.org.uk
NE1 7RU twitter: phillord
Phillip Lord
The way we have approached references on knowledgeblog.org is, whether
possible, to be independent of the editing environment; otherwise, you
have to replicate the entire tool chain.
For references, we have kcite working straight-forwardly with tools like
Mendely, Papers or best of all Emacs. The latter is easy to hack (took
10 lines of code I think). The others we added support by creating a
Citation Sytle Language format which feeds into kcite. Very easy, as it
just needs to dump the DOI into a short code. All very transparent to
the user; they just add a reference to their article.
As Martin says, combines very nicely with a CiTO/semantic
representation, because this can be coded entirely in the wordpress
layer. At the moment, I think, the only difficultly with building
references in wordpress is performance; the database queries are slow.
But, I think, this can be solved with a little bit of ajax, so that
database queries happen asynchronously.
Phil
Martin Fenner <fenner...@mh-hannover.de> writes:
> I would recommend to handle references indepent of any specific reference
> management tool. It would not be good to require authors to use a particular
> reference manager, particularly if the reference manager is not open source.
> Ideally the reference management implementation would be generic enough that
> it can connect to the most popular reference managers. There are different
> approaches for a generic reference management implementation already out
> there:
>
> * talk directly to CrossRef and PubMed (the Kcite plugin,
> http://wordpress.org/extend/plugins/kcite/)
> * use the WordPress Links Manager (my Wordpress Link to Link plugin,
> http://wordpress.org/extend/plugins/link-to-link/)
> * Embed reference information directly in HTML, using a standard format (
--
Carl Leubsdorf, Jr.
You wrote:
Wordpress sometimes get a little bit confused, as it expects posts and not articles (e.g. In the Dashboard)
- You can add Post Authors, Coauthors and an author in three different places, which is confusing
- The author template doesn’t seem to display the articles of that author or his biographical information
Further testing will tell how well Annotum plays with the scholarly plugins out there. My ePub Export plugin currently only works with posts and pages. It should be easy to make it work with Annotum – ideally with an ePub button next to the “PDF” and “XML” export buttons.
Best,
Martin
Am 25.06.11 03:01 schrieb "Carl Leubsdorf, Jr." unter <ca...@solvitor.com>:
Thanks Mark, and thank you for setting up a demo server!
I have a demo site at http://alpha.annotum.org but had not yet opened it for others to use. I had intended to use it to set up a bunch of sample content -- more of a display of what the system can do now for readers/viewers -- but I can open it up to registrations if people think that is useful.
As you explore, I'm happy to answer any questions about the review stuff -- the main thing to remember is that admins and editors can do almost anything, so for testing it is useful to create an author account or two and separate accounts for editors and reviewers.
It's also a bit hard at present to get a list of published articles, so I would recommend publishing a few and using the "recently..." widget in a sidebar. This will list the recently published articles.
Thanks again and I look forward to your feedback!
-C
Carl Leubsdorf, Jr.
William Gunn
The general sentiment Martin expresses, about avoiding platform lock-in, is a good one and one I fully agree with. Mendeley is just a good source for citation data as Open Data in this case.
Phillip Lord
The unfortunate reality of the situation at the moment is that
scientific bibliographic information is often held within closed
databases. Both Mendeley and crossref fall into this category.
It's something that I would like to address with kcite. At the moment,
you can cite things by DOI -- socially useful, but using a technology
that I feel is dreadful and entirely without purpose. In the end,
though, I want knowledgeblog articles to advertise and release their own
metadata, via http, with citation by URI.
We can't change the past, but it would be good if scientists in the
future released their papers in a way which allows automatic capture of
citation information direct from the source.
Phil
--
Jodi Schneider
Phillip Lord
> To cite data by URI, consider COinS [1][2], which was designed to implement
> the core of OpenURL in a Web environment.
> With OpenURL capture is not automatic but uses the citation, so is "direct
> from the source". There are COinS plugins for WordPress already; see [3] for
> a list.
Knowledgeblog already supports COinS. We ended up writing most of a
plugin ourself as the ones we found were mostly broken (they used
filters, but dumped to output stream, rather than added to $content if
you are interested).
But COinS is not a good solution for harvesting metadata. Part of the
reason for this is that it's got a nasty ugly syntax (yep, another
metadata standard I don't like!). The main reason, though, is that it is
embedded in document.
Imagine two blog posts A and B, with A referring to B. Both refer to
other posts/DOIs etc. A person comes along to post A to read it.
Wordpress decides therefore to retrieve the metadata for post B as
COinS. But this is embedded in post B. So wordpress retrieves post B,
from another wordpress (or itself). The WP hosting B doesn't know this
is computational, so retrieves all the metadata for its reference list.
Obviously this is bad, and worse if we have circular references. In the
first instance, I plan to publish metadata using the JSON that kcite
uses internally on a REST uri. Now, given a URI, I can retrieve the
metadata from the same server, but without retrieving the full text.
> I think Phil & I have agreed to disagree about DOI though. :) Its main
> advantage has been in getting publishers to make hyperlinked bibliographies
> which do in fact resolve.
Resolve in a complicated way, using another protocol, and to any old
random digital object.
> And while CrossRef is not open, you can access a lot of the data, even
> as linked data.
>
> To improve "automatic capture", ensuring that the metadata is machine
> readable from within the publication would help. Check your favorite
> publications: are they using XMPP metadata in PDFs? Does the HTML embed the
> metadata (as microdata, RDFa, etc)? Reporting problems -- to societies,
> librarians, and publishers -- can't hurt.
My problem is that there are too many standards, most of them very
complicated, and most of them not being used. CoINS, microdata,
microformats, RDFa, meta tags.
As always, I want standards to support me, not the other way around.
Phil
Jodi Schneider
Jodi Schneider <jschn...@pobox.com> writes:Knowledgeblog already supports COinS. We ended up writing most of a
> To cite data by URI, consider COinS [1][2], which was designed to implement
> the core of OpenURL in a Web environment.
> With OpenURL capture is not automatic but uses the citation, so is "direct
> from the source". There are COinS plugins for WordPress already; see [3] for
> a list.
plugin ourself as the ones we found were mostly broken (they used
filters, but dumped to output stream, rather than added to $content if
you are interested).
But COinS is not a good solution for harvesting metadata. Part of the
reason for this is that it's got a nasty ugly syntax (yep, another
metadata standard I don't like!).
The main reason, though, is that it is
embedded in document.
Imagine two blog posts A and B, with A referring to B. Both refer to
other posts/DOIs etc. A person comes along to post A to read it.
Wordpress decides therefore to retrieve the metadata for post B as
COinS. But this is embedded in post B. So wordpress retrieves post B,
from another wordpress (or itself). The WP hosting B doesn't know this
is computational, so retrieves all the metadata for its reference list.
Obviously this is bad, and worse if we have circular references. In the
first instance, I plan to publish metadata using the JSON that kcite
uses internally on a REST uri. Now, given a URI, I can retrieve the
metadata from the same server, but without retrieving the full text.
Resolve in a complicated way, using another protocol, and to any old
> I think Phil & I have agreed to disagree about DOI though. :) Its main
> advantage has been in getting publishers to make hyperlinked bibliographies
> which do in fact resolve.
random digital object.
My problem is that there are too many standards, most of them very
> And while CrossRef is not open, you can access a lot of the data, even
> as linked data.
>
> To improve "automatic capture", ensuring that the metadata is machine
> readable from within the publication would help. Check your favorite
> publications: are they using XMPP metadata in PDFs? Does the HTML embed the
> metadata (as microdata, RDFa, etc)? Reporting problems -- to societies,
> librarians, and publishers -- can't hurt.
complicated, and most of them not being used. CoINS, microdata,
microformats, RDFa, meta tags.
As always, I want standards to support me, not the other way around.
Phil
Phillip Lord
Jodi Schneider <jschn...@pobox.com> writes:
>> Knowledgeblog already supports COinS. We ended up writing most of a
>> plugin ourself as the ones we found were mostly broken (they used
>> filters, but dumped to output stream, rather than added to $content if
>> you are interested).
>>
>
> Better to tell this to the authors, than me. :)
It's such a small thing that it was easier to just fix it, to be honest.
I think we have released our plugin onto wordpress.com, so that's
another one for people to try!
>> > I think Phil & I have agreed to disagree about DOI though. :) Its main
>> > advantage has been in getting publishers to make hyperlinked
>> bibliographies
>> > which do in fact resolve.
>>
>> Resolve in a complicated way, using another protocol, and to any old
>> random digital object.
>>
>
> Right. :) There are better ways, but functional ones are ok until we have
> those. :)
My understanding is that the URI has been around for a while, and is
functional, and implemented on many platforms. Perhaps I am wrong about
this?
The bottom line is that 99% of (technical) users when faced with a DOI
just turn it into a URI, so that normal people can click on it. This
should probably tell you something.
BTW, I have absolutely no evidence at all for that statistic, so feel
free to contradict it!
>> As always, I want standards to support me, not the other way around.
>>
>
> It sounds like this will involve creating yet another standard -- but
> hopefully a unifying one!
People don't create unifying standards. Communities do!
Phil
Simon Cockell
>> Knowledgeblog already supports COinS. We ended up writing most of aIt's such a small thing that it was easier to just fix it, to be honest.
>> plugin ourself as the ones we found were mostly broken (they used
>> filters, but dumped to output stream, rather than added to $content if
>> you are interested).
>>
>
> Better to tell this to the authors, than me. :)
I think we have released our plugin onto wordpress.com, so that's
another one for people to try!
>> > I think Phil & I have agreed to disagree about DOI though. :) Its mainMy understanding is that the URI has been around for a while, and is
>> > advantage has been in getting publishers to make hyperlinked
>> bibliographies
>> > which do in fact resolve.
>>
>> Resolve in a complicated way, using another protocol, and to any old
>> random digital object.
>>
>
> Right. :) There are better ways, but functional ones are ok until we have
> those. :)
functional, and implemented on many platforms. Perhaps I am wrong about
this?
The bottom line is that 99% of (technical) users when faced with a DOI
just turn it into a URI, so that normal people can click on it. This
should probably tell you something.
BTW, I have absolutely no evidence at all for that statistic, so feel
free to contradict it!
People don't create unifying standards. Communities do!
>> As always, I want standards to support me, not the other way around.
>>
>
> It sounds like this will involve creating yet another standard -- but
> hopefully a unifying one!
Phil
--
Research Associate, Bioinformatics Support Unit,
Institute for Cell and Molecular Biosciences,
Faculty of Medical Sciences, Framlington Place,
Newcastle University,
Newcastle, NE2 4HH
Tel: +44 (0)191 222 7253 (Leech offices: Rooms M.2046/M.2046A - Mon-Wed)
Tel: +44 (0)191 246 4833 (Devonshire offices: Rooms G.26/1.16 - Thu/Fri)
Website: http://bsu.ncl.ac.uk/support
Helpdesk: sup...@bsu.ncl.ac.uk
Twitter: http://twitter.com/nclbsu
William Gunn
Best,
--
William Gunn | Head of Academic Outreach | +1 646 755 9862
http://www.mendeley.com/profiles/william-gunn
Mendeley Limited | London, UK
Registered in England and Wales | Company number 6419015
Phillip Lord
William Gunn <willia...@gmail.com> writes:
> Phil, can you explain to me why you say Mendeley is a closed database,
> when the catalog pages are public and there's a CC-BY license on
> everything available via the API? We really want this data to be as
> useful as possible to as many people as possible (that's the whole
> point!), so if there's some area that's really under-served by the
> current setup, please let me know and I'll pass that information back
> to the developers.
Perhaps I have misunderstood. I haven't had time to look at the terms
and conditions recently. I don't have a pressing need for the database
at the moment, so I wasn't planning on reading the legal stuff.
So, just quickly, tell me, can I download the entire database from
somewhere, install an independent copy of it, and release modified
versions of this copy?
Phil
William Gunn
Carl Leubsdorf, Jr.
Fenner...@mh-hannover.de
Von: wordpress-fo...@googlegroups.com [mailto:wordpress-fo...@googlegroups.com] Im Auftrag von Carl Leubsdorf, Jr.
Gesendet: Sonntag, 25. September 2011 20:41
An: wordpress-fo...@googlegroups.com
Betreff: Re: Annotum Alpha Released