# Wikis in scholarly communication
## Purpose

This page is meant to support some brain storming on the relative merits of paper-based and wiki-based scholarly communication, as discussed in a blog post that was later updated and expanded. Feel free to add to it, here or there, and to reuse it.

## Comparison between paper-based and wiki-based scholarly communication systems

| Feature of science communication | Paper-based practice | Comment | Wiki-based practice | Comment |
| ideas | | no timestemp system that is universal and transparent | | universal and transparent timestemp system |
| research design | | version control is tedious in collaborative studies | | version control is standard |
| research proposal | | version control is tedious in collaborative studies | | version control is standard |
| research funding | | | | |
| data acquisition | | | | |
| data analysis | | | | |
| manuscript writing | | version control is tedious in collaborative studies | | version control is standard |
| manuscript formatting | already largely standardized with LaTeX templates, less so with MS Word, OpenOffice and others | | standardized to some extent by the wiki syntax but not as much as a typical TeX style file allows | |
| reference formatting | already largely standardized with BibTeX, Endnote and similar | | standardized to some extent by the wiki syntax, via citation templates and automated reference wikification | |
| manuscript version tracking | requires external tools, e.g. Subversion, Google doc or a wiki | | standard | |
| choosing publication venue | scope and perceived "quality" of a journal | | there are not too many suitable wikis around and indeed, one of the purposes of publishing in a wiki would be to have all relevant information in one freely accessible spot, rather than in zillions of journals as in the paper-based world | |
| abstract | always written anew | only provided in a human-readable manner | always written anew | could easily be made machine-readable even after initial publication |
| introduction | always written anew, with some author-specific redundancy | | updated each time | |
| methods | always written anew, with some author-specific redundancy | | updated each time | |
| results | always written anew | only provided in a human-readable manner | always written anew | could easily be made machine-readable even after initial publication |
| discussion | always written anew, with some author-specific redundancy | | updated each time | |
| conclusions | | | | |
| references | separate section; never linked to online version, often not even with URI | tedious for both author and reader; often not balanced | link to online version is standard | could be facilitated by separated namespace for references |
| raw data | often missing, especially if it does not fit on paper (like audio or video files) | example case here | can be provided in the same wiki environment | |
| supplementary materials | often distributed into multiple files, not always integrable with paper | discussions here and here | not necessary - see above | |
| peer review | can be open, single-blind or double-blind; can be made available to the editors only or to a wider audience that could include the other reviewers, the authors, and the public | peer reviews are hard to track in their entirety, especially if non-published | can be open, single-blind or double-blind; can be made available to the editors only or to a wider audience that could include the other reviewers, the authors, and the public | simpler to track |
| author contributions | need to be written down specifically (particularly detailed example here) | | are always recorded; can possibly be automatically displayed (example in WikiGenes) | |
| errata | published separately (occasionally even more than once or as a complete republication), with no mention in the original paper version (another example here) | online versions frequently add a note about the updates but they are rarely incorporated into a corrected file that contains all of the information; non-text corrections further complicate the picture, as these files are often stored independently online and not reprinted (e.g. here or Fig. 1 in here) | can be easily corrected in the original location | a note about the update can be added easily, too |
| retractions | published separately, with no mention in the original paper version | online versions frequently (but not always) add a note about the updates (possibly hidden in the comments) but they are rarely incorporated into a corrected file that contains all of the information; "retractions at Wiley-Blackwell are now running at more than one a week" | can be easily corrected in the original location | a note about the update can be added easily, too |
| scientific correspondence | slow; danger of misunderstandings due to ambiguous wording | | quick; disambiguated hyperlinks to explanations of important concepts can reduce such friction | |
| access | often barred by subscription fees, generally with a delay after submission and/or peer review that may range from days to sometimes years | | open by default | immediate |
| reuse | copyright usually retained by the publisher, with important restrictions of reuse | | CC or GFDL licenses are standard | |
| metadata | error-prone and hard to correct | can be fixed in an easy, simple and transparent manner | | |
| outreach | roughly proportional to access and usability | | roughly proportional to access and usability | |
| impact | | | | |
| applications | | | | |
| teaching | | | | |
| resource use | | | | |

## Examples of scholarly wikis

A number of scholarly wikis are also contained in Wikipedia's list of online encyclopedias.
* OpenWetWare - Hosts biology 200+ lab web pages and protocols
* Scholarpedia - invitation-only cross-disciplinary wiki with real names, ISSN and classical anonymous peer review process that leads to stable versions
* Citizendium - cross-disciplinary wiki with real names and discipline-specific review process that leads to stable versions
* Encyclopedia of Earth - focus on Earth sciences, real names, discipline-specific review process that leads to stable versions
* Species-ID - biodiversity information; data facilitating the identification of species on Earth
* GroupPropsWiki - on Group Theory
* WikiSurgery - on surgery; spam-ridden
* Biopython - Python tools for computational molecular biology
* Tricky - on mathematical problem-solving techniques
* WikiEducator - for teaching purposes
* WikiGenes - for genes, with authorship tracking of text bits
* The Polymath wiki - highlights a series of collaborative contributions to a mathematical research question, ranging from its initial formulation to its solution in just a few weeks
* Quantiki - on quantum information
* Quizzes
* Mathematics Jobs Wiki
* SklogWiki on the thermodynamics of simple liquids, complex fluids, and soft condensed matter.
* Toxipedia - about drugs and toxicity
* Medpedia - about Health topics
* BioenergyWiki
* non-print media in environmental discourse
* NeuroLex - a glossary of neuroscientific terms
* AcaWiki - for scientific journal clubs online
* NeuronBank Wiki - for the description of neuronal cell lines and circuitry
* BredeWiki - neuroscience
* SubtiWiki - dedicated to Bacillus subtilis
* NMRWiki - for Magnetic Resonance (focus on spectroscopy)
* WikiPathways - for metabolic pathways
* wikiindex.org/Category:Science
* BioWikiFarm - a suite of wikis dedicated to biodiversity and related issues
* list of biowikis

## Desirable features of future scholarly wikis

For context, see here.
* Some system of peer review (basically, any wiki allows comments, annotations or formal reviews on talk pages of users or articles but these ratings should be featured more prominently; templates like those visualizing article status at Citizendium may help with that); this may be as simple as disallowing individuals to add information to Citizendium when the only available support is their own non-reviewed research published at OpenWetWare — the real name policy will minimize misuse
* Uploadability of all kinds of media that traditionally (if you can call a habit that barely is a decade old a tradition already) went along with paper-based publications as "supporting online information" (which would be easily integrated in an all-online non-printable article with no sharp space limitations).
* Stable versions for content that has undergone peer review (like the Approved Articles at Citizendium, or the results of the double phase review model at the OA journal ACPD/ACP), along with draft versions for anything else (including improvements to and updates of previous stable versions); like any non-protected page at the Wikipedias, these draft versions can serve as a playground, though a real-name policy would probably make it a more educational one
* Search engines that integrate or otherwise compare favourably with major scholarly search engines on the web (the already mentioned Google Scholar and PubMed as well as, say, the BioText Search Engine that searches Open Access text and images), also in terms of the updating frequency.
* pan-disciplinary scope, with consistent disambiguation of specialist terms (mainly but not fully achieved at Citizendium)
* Separate namespaces for references (already in use at the Dispersive PDE Wiki and the French Wikipedia, in test at Citizendium); as a side line, this would open up ways for new citation metrics, via the What links here function
* Separate namespaces for original research: Encyclopedic endeavours need expert input. This is most likely to be achievable if the encyclopedic activites can be integrated with the experts' workflow, e.g. via platforms like OpenWetWare.
* Attributability of contributions (automatically realized, though not in the traditional scholarly way, in any wiki with a real name policy like that at Citizendium, via the User contributions function; special arrangements exist at Scholarpedia and WikiGenes; OpenWetWare does allow nicknames but real names prevail; the Wikiversities have basically the same user name policy as the Wikipedias)
* Easy download of selected sets of pages for local archiving or analysis.
* Licenses that allow unrestricted reuse and derivative work if the original source is properly acknowledged (typically CC-by-SA or the older GFDL, both of which have been made compatible now)
* Resource-effective design (see also discussions on the energy use of the internet and individual websites). This overview may also help in working out an ecological footprint scheme applicable to research, as described previously.
* integration with the non-scholarly world (certainly achieved in the Wikipedias and Citizendium), particularly with students (cf. the Eduzendium initiative at Citizendium) and non-English contents
* Automation of the formatting, as already common in non-wiki environments, e.g. with LaTeX templates, for which collaborative editing environments exist too. None of the wikis we know comes close to that, albeit templates are heavily used at the various Wikipedias and, to a lesser extent but in a more consistent manner, at Citizendium; they seem to be rather rarely used on smaller or more specialized wikis. The same applies to references, though automated wikification has already progressed considerably here, despite the lack of wiki export functions at publisher's sites (or of suitable XML-to-wiki converters for those who provide XML)
* Integration with mind maps (which structure knowledge) and databases (which harbour bits of knowledge that do not make much sense without a broader context).
* Distributed version control, e.g. via git (Warning: open science is not open source)

## Alternatives to wikis

* Basically anything that is more WYSIWYG (e.g. Open Office, MS Word), more real time (e.g. Etherpad/ Google Doc/ Google Wave Sites / Google Knol) or more integrated with references or other non-text elements of publishing, or more semantic.
* Encyclopedia of Life: focussing on species descriptions, it is not a wiki. EoL is more similar to a news aggregator, using semantic meshup pulled from associated content sites