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CODE4LIB  November 2010

CODE4LIB November 2010

Subject:

WordPress + research papers - wishlist

From:

Jodi Schneider <[log in to unmask]>

Reply-To:

[log in to unmask]

Date:

Fri, 12 Nov 2010 14:15:26 +0000

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text/plain

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text/plain (184 lines)

The WordPress platform is a good place to start for building on research
papers.

I'm forwarding your WordPress module wishlist to Code4Lib:

I would be interested in these two
> Wordpress modules:
> a) an author module that integrates with the ORCID researcher
> identifier system. Manuscript authors could provide their ORCID
> credentials when starting a document, and there would be no need to
> provide author information at the time of manuscript submission. This
> module would also allow all coauthors to approve a manuscript before
> submission. The system should also define the role of the author in
> the manuscript ("provided data", "did experiment X", etc.).
> b) a citation module that extends the current Wordpress functionality
> of providing links. The module should provide rich formating of
> citations (using the citation style language CSL), should verify
> citations, should add meaning to citations (using the Citation
> Ontology CiTO), and should allow citations of specific parts of a
> paper or dataset.


Code4Lib folks, for context see
https://sites.google.com/site/beyondthepdf/

Thought of y'all in part because the Code4Lib Journal uses some WordPress
customizations:
http://wiki.code4lib.org/index.php/Code4Lib_Journal_WordPress_Customizations

-Jodi

---------- Forwarded message ----------
From: Martin Fenner <[log in to unmask]>
Date: Fri, Nov 12, 2010 at 12:37 PM
Subject: Re: Workshop Deliverables?
To: Beyond the PDF <[log in to unmask]>


I'm very much enjoying this discussion, and it is still more than two
months to go before we actually meet in person. I also like the focus
of delivering something meaningful at the end of the workshop rather
than just having a very interesting conversation about topics beyond
the PDF. Earlier on we have talked about some of the practical aspects
to make this work, and that included incentives for the individual
researcher and tools that make the creation of a scholarly paper
easier and not more difficult. I would like to add another
requirement, and that is that all scholarly tools should built on
standard tools we already use in other domains, and not build
something from scratch. The reason for that is that the scholarly
community is relatively small, and the larger community is already
working on not on all, but many of the same issues. And it has been
stated from the very beginning that we want to build open source
tools.

I would propose that we think about the technology platform that is
the best starting point for a tool we can build at or shortly
following the workshop. There are many potential candidates (Google
Wave was also on that list for a while). Lemon8-XML from the Public
Knowledge Project (http://pkp.sfu.ca/lemon8) would be one good
candidate. Right now it is a tool to convert documents in Microsoft
Word or Open Office formats into the NLM-DTD to publish them with the
Open Journal Systems journal submission system. But in the last few
weeks I realized that for me the ideal platform for an authoring tool
is actually Wordpress. JISC recently funded the Knowledge Blogs
project by Phil Lord (http://researchdata.jiscinvolve.org/wp/
2010/08/02/new-jiscmrd-projects-citing-linking-and-integrating-
research-data/) that will build a lightweight publication system. He
would be able to say much more about the potential and obstacles of
that platform. The main reason for me to pick Wordpress is that it
already solved many of the problems we would have to work on when
building a new authoring tool, as it is a mature and well-documented,
web-based, multiuser publishing platform. Most importantly, I think it
is a platform that authors will like and actually use.

So I propose that as one workshop deliverable we built several
extensions (widgets) to the Wordpress system. The modular system of
the Wordpress platform makes it ease to start several sub-projects
that work on different aspects of the scholarly paper. And it is
certainly possible to deliver something using that platform until the
end of 2011. Code that went into building these Wordpress modules
could be reused for other porjects. I would be interested in these two
Wordpress modules:

a) an author module that integrates with the ORCID researcher
identifier system. Manuscript authors could provide their ORCID
credentials when starting a document, and there would be no need to
provide author information at the time of manuscript submission. This
module would also allow all coauthors to approve a manuscript before
submission. The system should also define the role of the author in
the manuscript ("provided data", "did experiment X", etc.).

b) a citation module that extends the current Wordpress functionality
of providing links. The module should provide rich formating of
citations (using the citation style language CSL), should verify
citations, should add meaning to citations (using the Citation
Ontology CiTO), and should allow citations of specific parts of a
paper or dataset.

Martin Fenner
Hannover Medical School
ORCID Initiative
http://blogs.plos.org/mfenner

On 12 Nov., 04:32, Rebholz <[log in to unmask]> wrote:
> Hi all,
>
> I do enjoy the discussion although I am not always online enough to be
> aware of all discussion points (I will backtrack during the day).
>
> The key outcomes of the workshop in my eyes would be:
>
> (1) Can we define / sketch a document format that enables distribution,
> exploitation according to functional requirements (that have to be
> defined, sigh) for a significant number of involved parties?  These
> functional requirements could be (a) openness for distribution and
> processing, (b) adding / exploiting meta-data, (c) following /
> combinding given standards, new standards.  It is also acceptable to
> have 2-3 document formats that allow transformation forth and back, if
> each of these standards or almost all of them come at a reasonably low
> overhead expense and forward/backward transformation is enabled. PDF is
> certainly more the end product than a working document format (well,
> some highend developers might want to disagree).
>
> (2) Can we define an infrastructure of tools / components that support
> distribution / exploitation of the documents and literature? A number of
> components have already been named and it will be an interesting
> discussion to see, how they reconcile.  There is always the notion that
> it should work to put everything together, which is certainly an obvious
> trap.
>
> (3) What tools and resources promote (1) and (2) and embed both into the
> general public / research community, provide benefits to consumers of
> documents (researchers, authors, IT solutions) and producers
> (publishers, authors again, IT groups for tool development).
>
> Let's see what I find in the other emails that fits to these sections.
> I have seen the discussion about RDF and Triples.  I have not seen any
> arguments about Pubmed Central XML, which is actually more difficult
> than it looks.  Certainly DOIs, URIs, Purls, standard XML (PMC) and
> public RDF schemas are all great, but if we talk about interoperability
> we end up in a pretty bleak IT wholesale.
>
> Apologies if I forgot any open standards where somebody in this
> discussion group feels very strong about.
>
> Best,
>      -drs-
>
> On 12/11/2010 06:13, Phil B wrote:
>
>
>
>
>
> > The dialog that has ensued so far is brilliant and 69 days to go
> > before we even get to talk face to face. I sense that in typical
> > workshop style we will easily be able to claim success - people make
> > new contacts, a lot of ideas are floated around and people go off and
> > do better in their individual endeavors because of it. I also sense it
> > as an opportunity to do something more as a collective effort. So this
> > post is to get the discussion going on what that something might be.
> > Here are some thoughts.
>
> > We take whatever minimum consensus can be reached at the meeting on
> > the various aspects of scholarly communication you have been
> > discussing and agree to do something with it as a group that is going
> > to broadly impact scholars who have no idea what a triple is, or RDF,
> > or nanopublication etc. This could be an application (killer?) that is
> > identified at the meeting, it could be a new style publication
> > identifiable in the current reward system, it could be some kind of
> > hub integrating data, knowledge about that data etc. which is going to
> > drive the need to recognize a new kind of reward system etc etc. Some
> > of these ideas would presumably be applied to a specific domain,
> > others could be applied across domains.
>
> > What do you think we should deliver from this workshop?
>
> > Cheers../Phil
>
> --
> Dietrich Rebholz-Schuhmann, MD, PhD - Research Group Leader
> EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD (UK)
>   - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> TM support:www.ebi.ac.uk/Rebholz-svr| [log in to unmask]

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