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JATS Con Paper Proposal
Here's where we can collaborate on a paper proposal for presenting this project at JATSCon 2012 (October 16 & 17, 2012).
Deadline for the submission is Friday, May 18, and the submission form is here.
We got an extension on the submission until Sunday, May 20.
- Seldom does the online version add value: corrections cannot be made directly on the article, specialists identifying flaws with the methodology are unable to share their views through comments, and new interpretation of the data based on new findings cannot be incorporated into the original work. Errors (conceptual or factual) in the original text are often perpetuated in subsequent articles. - Daniel Mietchen
JATS-to-Mediawiki - A conversion tool for use in the Encyclopedia of Original Research Nobody knows what the Encyclopedia of Original Research is about, so there could probably be a better selling point, e.g. "The JATS-to-Mediawiki converter - a basic tool to render PubMed Central articles editable."
(200-word description of your paper, mentioning the key topic(s) or findings. This will be the basis of the paper's description in the conference program.)
Science is already a wiki if you look at it a certain way. It's just a really, really inefficient one. -- John Wilbanks.
A large and continuously growing corpus of scientific literature is stored in JATS format, and a considerable proportion thereof is available under open licenses. The JATS-to-Mediawiki software is currently being developed to convert articles from JATS XML into MediaWiki XML. MediaWiki is a free platform used in many applications, including Wikipedia. Conversion of scientific articles into this format will allow them to live on in such collaborative editing environments.
As such, the JATS-to-Mediawiki converter is an integral component of the Encyclopedia of Original Research (EOR), which is a project designed to redeploy the existing and newly published openly licensed scientific literature in a way that allows it to become a living, dynamic record of thematically interlinked articles. The primary goal of the EOR project is to develop a platform that is able to at once capture and archive the open scientific literature such that the original work is preserved, and at the same time allow it to become dynamically and collaboratively editable.
The JATS-to-Mediawiki software itself, as with the rest of the EOR project, is being developed completely in the open, and is hosted on GitHub, at https://github.com/konrad/JATS-to-Mediawiki/.
(Detailed description of your paper/proposal. This description must be long enough, and detailed enough, that the peer reviewers will be able to evaluate the fit of your topic in the conference as a whole and your qualifications to speak on this topic.)
Knowledge is deeply rooted in context and collaboration. We propose that publication systems should be built so that they facilitate and encourage the expression of those attributes. A record of the context and collaboration is the centre stone of the preservation of the cultural heritage of science. - Daniel Mietchen
Traditional publications do not reflect (nor do they have room for) continual updating and revision of the published material. As previously discussed (Mietchen et al. [3]) Wikis could play a central role in the future of scholary publishing. They make continuous improvement of research articles possible and inherently offer tracking of author contributions. Wikipedia policy, however, does not allow its authors to contribute content that includes original research.
An example of a dynamically-editable platform for peer-reviewed scientific literature that is already deployed, is the Species ID wiki. At JATSCon 2010, we heard a talk by Terence Catapano on the TaxPub DTD and ZooKeys, a publication of Pensoft. ZooKeys articles, when they are published, are simultaneously deployed to the Species ID wiki, where they exist as versioned wiki pages, which can be dynamically updated by qualified scientists as new information becomes available. Author contributions can be tracked and attributed.
The Encyclopedia of Original Research aims to generate a bridge between the old static and new continuously improved publishing model by importing open access articles stored as JATS XML in a MediaWiki based system. For this purpose the tool JATS-to-Mediawiki was developed which implements a XSLT based conversion of JATS XML to MediaWiki XML format [4]. The generated MediaWiki XML files can be imported by any MediaWiki instance. After such an import the articles can be edited easily via the MediaWiki web interface.
The current state of JATS-to-Mediawiki is focused of the NISO JATS version 0.4 but in future the tool will be able to handle also predecessor versions (NLM 1.0 to 3.0).
(Any related information you would like to provide to the conference committee as they select papers for the conference.)
[1] TaxPub: An Extension of the NLM/NCBI Journal Publishing DTD for Taxonomic Descriptions. T. Catapano. JATS-Con Proceedings. (2010) http://www.ncbi.nlm.nih.gov/books/NBK47081/
[2] Interlinking journal and wiki publications through joint citation: Working examples from ZooKeys and Plazi on Species-ID. Penev L, Hagedorn G, Mietchen D, Georgiev T, Stoev P, Sautter G, Agosti D, Plank A, Balke M, Hendrich L, Erwin T. ZooKeys 90: 1-12. (2011) http://dx.doi.org/10.3897/zookeys.90.1369
[3] Wikis in scholarly publishing. Information Services and Use. Mietchen D, Hagedorn G, Förstner KU, Kubke MF, Koltzenburg C, Hahnel M, Penev L (2011) 31(1-2) : 53–59, doi: 10.3233/ISU-2011-0621. Versioned wiki page: 2012-04-13, version 23217, http://species-id.net/w/index.php?title=Wikis_in_scholarly_publishing&oldid=23217
[ Please provide your author biography here. ]
Konrad U. Förstner
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Affiliations:
- Research Center for Infectious Diseases, University of Würzburg, Germany
- Institute for Molecular Infection Biology, University of Würzburg, Germany
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Bio: After studying biochemistry and computer science at the University of Greifswald, Germany, Konrad U. Förstner did a PhD in bioinformatics about metagenomic data analysis in the group of Peer Bork at the EMBL in Heidelberg, Germany. Since 2011 he is a postdoc at the Research Center for Infectious Diseases and the Institute for Molecular Infection Biology at the University of Würzburg, Germany. Besides his main research topic - the computation analysis of next-generation-sequencing data - he tries to promote the idea of open science.