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JATS Con Paper Proposal
This is a record of a proposal for presenting this project at JATSCon 2012 (October 16 & 17, 2012). We drafted this proposal here in the open.
Submitted this version on Monday, May 21, 7:25AM. It got rejected, unfortunately, on June 27.
JATS-to-Mediawiki - a conversion tool to make the PMC Open Access subset dynamically 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 allows them to live on in such a collaborative editing environment.
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 capture and archive the open scientific literature such that the original work is preserved, while at the same time allow it to become dynamically and collaboratively updated.
The JATS-to-Mediawiki software, as with the rest of the EOR project, is being developed in an open, collaborative manner, 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.
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. [1]) wikis could play a central role in the future of scholary publishing. They make continuous improvement of research articles possible, while allowing for automated tracking of author contributions. The most widely used wiki, Wikipedia, is not suitable for this role, however, because Wikpedia policy does not allow authors to contribute content derived from 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 [2][3]. 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 be a bridge between the old, static form of journal article publishing, and a new publishing model afforded by Web 2.0 technologies, that involves continuous, fine-grained improvements to the published record. It will do this by importing open access articles stored as JATS XML into a MediaWiki-based system. For this purpose, the JATS-to-Mediawiki tool was developed. This tool implements an XSLT-based conversion of JATS XML into MediaWiki XML format. The generated MediaWiki XML files can be imported by any MediaWiki instance. After such an import, the articles can be edited via the MediaWiki web interface, thereby creating a versioned history of the topic at hand.
[1] 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
[2] 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/
[3] 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
Any related information you would like to provide to the conference committee as they select papers for the conference.
Authors are listed in alphabetical order.
[ Please provide your author biography here. ]
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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 computational analysis of next-generation-sequencing data - he tries to promote the idea of open science.
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Affiliation:
- NCBI/NLM/NIH, contractor with A-Tek, Inc.
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Bio: Chris Maloney is a web developer working for NCBI's PMC and Bookshelf resources. He has worked with XML technologies for over ten years, and has more recently become interested in issues surrounding open access and open science.
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Affiliations:
- EvoMRI Communications, Jena, Germany
- Open Knowledge Foundation Germany, Berlin, Germany
- Pensoft Publishers, Sofia, Bulgaria
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Bio: Daniel Mietchen is a freelancing scientist. Trained in Biophysics at the Humboldt University in Berlin, he did a PhD in Physics at the University of the Saarland, focusing on applications of Magnetic Resonance Imaging to dehydrated biological systems. Thematically, his research ranges from fossils and embryonic development to cold hardiness, music perception, brain morphometry and vocal learning. This entails the transdisciplinary collaboration with researchers from around the globe, which sparked the initial interest in what is his current focus - the integration of research workflows with the World Wide Web, particularly by way of collaborative platforms like wikis. He currently is the Wikimedian in Residence on Open Science, hosted by the Open Knowledge Foundation Germany.