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== Background ==
{{AccountNotLive}}
{{Image|PLoS-ad-putting-research-in-context.jpg|right|468px|Do journals provide sufficient contextualization for research?}}
{{:User/Daniel_Mietchen/COASP2010/Template}}
*For technical reasons, [[User:Daniel Mietchen/Talks/LSWT 2010/Integrating wikis with scientific workflows/Publishing|publishing]] was historically a separate step, performed about once per iteration of the research cycle


*Publishing every relevant bit of information immediately at each step is technically feasible now, and the remaining hurdles are cultural ones.
{{TOC|right}}
''This page hosts supplementary notes for a [[User:Daniel Mietchen/Talks/COASP 2010/Wikis as platforms for scholarly publishing|talk]] in the [http://www.oaspa.org/coasp/sessions.php Session] on Editorial Innovation in [[open access|OA]] [[academic publishing|Publishing]] at [http://www.oaspa.org/coasp/ COASP], August 23, 2010, Prague. I hope it will be useful during the Q & A session and for later reuse.''


*Wikis allow for systematic linking and thus enhanced contextualization (sidenote: some have argued that [http://www.readwriteweb.com/archives/links_in_text.php links are distracting])
*[http://blogs.ubc.ca/brian/2010/07/viva-la-wiki/ Overview] of the evolution of wikis and wiki-like environments
:Mentions MediaWiki plugin for Wordpress
:Etherpad
:Google Docs
*[http://thisiscolab.com/blog/dear-scientists-stop-duplicating-work/ Dear Scientists, Stop Duplicating Work]
==Wikis as platforms for science communication==
*Wikis can be used, in principle, for any aspect of scholarly communication, as detailed in [http://en.wikiversity.org/wiki/Wikis_in_scholarly_communication this comparison of wiki- and paper-based communication systems] and the [http://ways.org/en/blogs/2009/sep/29/what_would_science_look_like_if_it_were_invented_today_part_ii_knowledge_structuring related blog post].
*[[User:Daniel Mietchen/Talks/Integrating wikis with scientific workflows|Examples exist]] for all steps of the [[Scientific_method#Components_of_the_scientific_method|research cycle]], except successful applications to major funders (see [[User:Daniel Mietchen/Talks/Integrating wikis with scientific workflows/Funding|this overview]] for some attempts)
*Benchmark: [http://wiki.ubc.ca/Size_of_Wikipedia English Wikipedia]
:[http://ragesoss.com/blog/2006/11/20/top-10-reasons-why-academics-should-edit-wikipedia/ Top 10 Reasons Why Academics Should Edit Wikipedia]


==Wikis as platforms for scholarly publishing==
==Wikis as platforms for scholarly publishing==
{{Image|Encyclopedia of Earth Ad.jpg|right|250px|Encyclopedia of Earth — a wiki with overview articles reviewed by experts, available under [http://creativecommons.org/licenses/by-sa/2.5/ CC-BY-SA]}}
===Functions of scholarly publishing===
*The idea is not new — [http://meatballwiki.org/wiki/WikiSciencePublication WikiSciencePublication] stated in 2006:
''See also [http://ff.im/p0D6y this Friendfeed thread].''
:"Somewhere at the fringe of science, someone will start using wiki publishing for science publishing."
*Inform about new knowledge
:See also [http://en.wikiversity.org/wiki/Wikiversity:Publishing_original_research Wikiversity:Publishing original research]
*Archive existing knowledge
*(Make profit)


*Most variants of [http://en.wikipedia.org/wiki/Wiki_software wiki software] can handle [[User:Chris Key/Sandbox/Proposal: Overhaul of user rights#Summary_of_Rights_Given_to_Each_User_Group|user rights]] in great detail, so as to allow '''implementation of basically any [http://www.the-scientist.com/article/display/57601/ kind of peer-review system]'''
====More detailed listings====
''Just for reference''
*Essential elements of science publishing:
**Research
**Documentation
**Making things public
**Integration with previous and future knowledge
**Discussion


*Lab reports: [http://pubs.acs.org/doi/abs/10.1021/ed800022b Lab reports]
*Seven quality indicators to strive for in an ideal peer review system (per  [[CZ:Ref:Jefferson 2002 Measuring the quality of editorial peer review|Jefferson et al., 2002]])
#importance,
#usefulness,
#relevance,
#methodology,
#ethics,
#completeness
#accuracy of an article
#accountability (added by Peter Frishauf  in [http://www.patientpower.info/audio/webcast/JOPM_Chap4.mp3 part 4])


*Conferences: [http://meta.wikimedia.org/wiki/Wikimania_2010 Stand-alone site] / [[Open Knowledge Conference/Program/OKCon 2010|contextualized schedule]] / [http://www.libsuccess.org/index.php?title=Wiki_World talks], [[User:Daniel Mietchen/Talks/LSWT 2010/Integrating wikis with scientific workflows|contextualized talks]] and [[:Image:Neuroimaging workflow.png|Posters]] (possibly also as clickable imagemaps, like [[User:Daniel Mietchen/Talks/Integrating wikis with scientific workflows|here]]), [http://wiki.ubc.ca/index.php?title=Resource_Management_Framework&oldid=33728#Process:_the_problem.2C_the_pieces_and_the_tradeoffs presentations]
*[http://www.springerlink.com/content/7162335157t83538/ Selection, Finance, Organization, Aggregation, Marketing]
#"Selection: it has been said that publishers are better defined by what they do not publish rather than by what they do. A key part of what publishers do lies in the editorial process--selection, acquisition, commissioning."
#"Finance: publishers take the--sometimes considerable--financial risk in publishing, and can reasonably expect to make a return broadly commensurate with that risk."
#"Organization: at the core of the publisher's role is the co-ordination of all the developmental processes that turn the author's raw material into a finished product for the market. This is an often-overlooked part of the publisher's art. It perhaps becomes most obvious only by its absence."
#"Aggregation: it may seem odd to talk about aggregation as being part of a traditional publisher's role, but we would argue that there is nothing new about aggregation of content. The book and journal publishing supply chains are focused on aggregating the works of individual authors--with the ultimate aggregators in the physical world being bookstores and libraries. It is typically to these points of aggregation that consumers go to purchase or borrow the particular item to which they want access."
#"Marketing: last, perhaps, but certainly not least. Marketing is selfevidently a crucial element of the publisher's role. Here, we mean marketing in its broadest sense ensuring that products are appropriate to the markets for which they are published as well as promoting the products to the markets themselves. In this context, we see marketing as including both customer service and distribution channel management."
*[http://www.springerlink.com/content/ew46l71366t4348q/ "for practical purposes we can define publishing to include, along with page design and typesetting, the functions of editing, manufacturing, advertising, selling, warehousing, shipping, billing, collection, and other aspects of "valued added" and "Who will keep the gates? How? To what end?] (1988)


*Research papers: [http://www.landesbioscience.com/journals/rnabiology/guidelines/ Accompanied by wiki article] ([http://xfam.wordpress.com/2010/06/30/plans-for-rfam-2010-2011/ progress report]), [[User:Daniel Mietchen/Research/In Vivo Assessment of Cold Adaptation in Insect Larvae by Magnetic Resonance Imaging and Magnetic Resonance Spectroscopy|contextualized on-wiki]], [http://www.plosmedicine.org/article/info%3Adoi%2F10.1371%2Fjournal.pmed.0040173#abstract2 links to wikis amongst other sources], [http://www.biomedcentral.com/1471-2105/11/220 integrated into database]


*Review articles: [http://www.scholarpedia.org/article/Magnetic_resonance_imaging Scholarly] / [http://www.eoearth.org/article/Surface_weather_maps Outreach]


*[http://openwetware.org/wiki/User:Daniel_Mietchen/Notebook/Open_Science/2010/07/26#Wikis_can_act_as_publication_filters_for_new_research Wikis can act as publication filters for new research]
:See also [http://friendfeed.com/science-2-0/b3d97e5c/can-computers-help-scientists-with-their Can Computers Help Scientists With Their Reading?]


*[http://en.wikibooks.org/wiki/Wikibooks:Featured_books Books]


*[http://acawiki.org/ References]
==Quality assessment==


*[[User:Daniel_Mietchen#Research_publications|Publication lists]] (incl. supplementary materials and in principle direct links to the raw data)
=== Traditionally ===
Single-blind or double-blind or open peer review, with the reviewers or even authors always or optionally, temporarily or permanently remaining anonymous, with simple accept/ revise/ reject decisions or interactive two-stage or multi-stage discussions, in public or hidden from it (possibly even in part), before and/ or after formal publication.


*[http://www.quantiki.org/wiki/Open_Problems To-do lists for a whole discipline]
Some non-wiki examples:
:See also [http://colabscience.com/ CoLabScience]
#[http://publications.copernicus.org/ Copernicus journals]
#[http://www.plos.org/journals/ PLoS journals]
#[http://www.frontiersin.org/ Frontiers journals]
#[http://www.biomedcentral.com/browse/journals/ BMC journals]
#[http://www.semantic-web-journal.net Semantic Web journal]
#[http://math.rejecta.org/ Rejecta Mathematics]
#[http://www.webmedcentral.com/ WebMedCentral]


*built-in [[article-level metrics]] at bottom of page and via [[Special:WhatLinksHere|What links here]] (which could also be used for other pages, e.g. those hosting images, references, or datasets), author-level metrics via [[Special:Contributions/Daniel_Mietchen|Special:Contributions]], further aggregation possible (e.g. at the level of [http://openwetware.org/wiki/User:Carl_Boettiger/Notebook/Stochastic_Population_Dynamics#Collected_Literature research projects], [http://usefulchem.wikispaces.com/ labs] or [http://en.citizendium.org/wiki?title=Special:RecentChangesLinked&target=Category%3ABiology_tag thematic workgroups])
*Problems from [http://www.the-scientist.com/article/display/57601/ I hate your paper]:
#Reviewers are biased by personal motives
#Peer review is too slow, affecting public health, grants, and credit for ideas
#Too many papers to review


*[http://www.wittylama.com/2009/09/wikipedia-journal/ Wikipedia Journal]
*Respective solutions:
 
#Eliminate anonymous peer review ( Biology Direct, BMJ, BMC); run open peer review alongside traditional review (Atmospheric Chemistry and Physics); judge a paper based only on scientific soundness, not impact or scope (PLoS ONE)
*[http://peanutbutter.wordpress.com/2008/08/19/is-a-knol-a-scientific-publishing-platform/#comment-1492 Knol] shares some aspects with wikis and blogs and is already in use for [http://www.ploscurrents.org/ PLoS Currents].
#Shorten publication time to a few days (PLoS Currents Influenza); bypass subsequent reviews (Journal of Biology); publish first drafts (European Geosciences Union journals)
#Recycle reviews from journals that have rejected the manuscript (Neuroscience Peer Review Consortium); wait for volunteers (Chemical Physics Letters); reward reviewer efforts (Biology Direct, BMC, Frontiers, ACP)


==Wikis as platforms for Open Access publishing==
*From [[NP complexity class|P≠NP]]:
*The majority of wiki platforms are [[open access]] by default
:[http://cameronneylon.net/blog/p-≠-np-and-the-future-of-peer-review/ P ≠ NP and the future of peer review]
:[http://techdirt.com/articles/20100812/03472410604.shtml Rethinking Peer Review As The World Peer Reviews Claimed Proof That P≠NP]
::"Apparently, people are realizing that a much more open post-publication peer review process, where anyone can take part, is a lot more effective"
::[http://techdirt.com/article.php?sid=20100812/03472410604#c255 "we have very little evidence that pre-publication closed peer review is any good at any of these things. In a sense, as scientists this should be obvious. You would never make a strong claim based on a very small number of measurements, which rarely come to the same result, and then hide the actual data away where no-one can see it. Yet this is exactly what we do with pre-publication peer review in most cases."]


*Stresses the re-use part of CC licenses (e.g. for [[Chordoma|images]]) — an aspect of OA publishing that does not receive much attention outside research blogs (cf. [http://www.damtp.cam.ac.uk/user/jono/item/toc.html detailed discussion] with respect to the [http://www.aps.org/ American Physical Society], [http://arxiv.org/ arxiv] and [http://www.quantiki.org/ Quantiki], and the [http://rmp.aps.org/edannounce/PhysRevLett.101.140001 final outcome: APS authors keep copyright over derivative works]). While the main purpose of such licensing is certainly to make the research available to other specialists working in the field, they also make the research available to scientists from other fields (not just in academia) as well as non-scientists (teachers, entrepreneurs, media, patient groups or hobbyists).
=== On wiki ===
:Examples: [[Gyrification]], [[Surface-based morphometry]] and [[Chordoma]]
In principle, any system of (peer) review can be implemented on a wiki, by detailed management of [[User:Chris Key/Sandbox/Proposal: Overhaul of user rights#Summary_of_Rights_Given_to_Each_User_Group|user rights]]: The usual  
:Also note that [http://dx.doi.org/10.3389/neuro.11.025.2009 Fig. 3 of http://dx.doi.org/10.3389/neuro.11.025.2009] and [http://dx.doi.org/10.3389/fnins.2010.00020 Fig. 2(III) of http://dx.doi.org/10.3389/fnins.2010.00020] explain the same thing, original to neither papers
 
*Incompatibility of wikis and closed-access publishing
:[http://friendfeed.com/auditory-motor-coupling/2d9a52d1/reuse-of-images-from-wikipedia-in-copyrighted re-use of CC-BY-SA content in copyrighted papers]
 
==Quality assessment==
In principle, any system of peer review can be implemented on a wiki, by detailed management of [[User:Chris Key/Sandbox/Proposal: Overhaul of user rights#Summary_of_Rights_Given_to_Each_User_Group|user rights]]: The usual single-blind as well as double-blind or open peer review, with the reviewers or even authors always or optionally, temporarily or permanently remaining anonymous, with simple accept/ revise/ reject decisions or interactive two-stage or multi-stage discussions, in public or hidden from it (possibly even in part), before and/ or after formal publication.


Some wiki examples:
Some wiki examples:
Line 76: Line 83:
#[[Citizendium]]
#[[Citizendium]]


Some non-wiki examples:
 
#[http://publications.copernicus.org/ Copernicus journals]
 
#[http://www.plos.org/journals/ PLoS journals]
 
#[http://www.frontiersin.org/ Frontiers journals]
#[http://www.biomedcentral.com/browse/journals/ BMC journals]
#[http://www.semantic-web-journal.net Semantic Web journal]
#[http://math.rejecta.org/ Rejecta Mathematics]
#[http://www.webmedcentral.com/ WebMedCentral]


==Business models==
==Business models==
*Main ones: author-pays, (partial) subscription, philanthropy, advertising, premium services
*Main ones: author-pays, (partial) subscription, philanthropy, advertising, premium services
*Micropayments [http://ff.im/oyzlk Science-specific]/ [http://flattr.com/ general]?


==Opportunities==
==Opportunities==
Line 103: Line 106:
*[http://chem-bla-ics.blogspot.com/2010/06/critical-mass-for-open-notebook-science.html Automated pre-population from databases]
*[http://chem-bla-ics.blogspot.com/2010/06/critical-mass-for-open-notebook-science.html Automated pre-population from databases]


==Notes==
==Quotes==
*Essential elements of science publishing:
**Research
**Documentation
**Making things public
**Integration with previous and future knowledge
**Discussion
 
*Seven quality indicators to strive for in an ideal peer review system (per  [[CZ:Ref:Jefferson 2002 Measuring the quality of editorial peer review|Jefferson et al., 2002]])
#importance,
#usefulness,
#relevance,
#methodology,
#ethics,
#completeness
#accuracy of an article
#accountability (added by Peter Frishauf  in [http://www.patientpower.info/audio/webcast/JOPM_Chap4.mp3 part 4])
 
----
*use screenshots of Recent changes from mainspace around midnight from WP, EoE, SP, CZ, WE & OWW & Knol
 
----
*Problems from [http://www.the-scientist.com/article/display/57601/ I hate your paper]:
#Reviewers are biased by personal motives
#Peer review is too slow, affecting public health, grants, and credit for ideas
#Too many papers to review
 
*Respective solutions:
#Eliminate anonymous peer review ( Biology Direct, BMJ, BMC); run open peer review alongside traditional review (Atmospheric Chemistry and Physics); judge a paper based only on scientific soundness, not impact or scope (PLoS ONE)
#Shorten publication time to a few days (PLoS Currents Influenza); bypass subsequent reviews (Journal of Biology); publish first drafts (European Geosciences Union journals)
#Recycle reviews from journals that have rejected the manuscript (Neuroscience Peer Review Consortium); wait for volunteers (Chemical Physics Letters); reward reviewer efforts (Biology Direct, BMC, Frontiers, ACP)
 
----
*Mention possibility of linking to Open Access funding, as per [http://ff.im/oyzlk Microfinancing for science]
----
*[http://project.liquidpub.org/ Liquid Publications] — the editable web
----
On the cover image: Journals are not essential to a wiki system described here, as their function of conveying new information would go away, but they still have their role in turning edit histories into stories, and in framing debates, for which wiki talk pages are not ideal.
----
Mention alternatives to wikis:
*Etherpad,
*Google docs
*ScribTeX
*[http://wordpress.org/extend/plugins/buddypress-group-wiki/ Buddypress]
 
===Quotes===
From [http://www.patientpower.info/JoPM.asp the JoPM peer review discussion] ([http://ff.im/oVHcb my comments])
From [http://www.patientpower.info/JoPM.asp the JoPM peer review discussion] ([http://ff.im/oVHcb my comments])


Line 169: Line 127:
"I believe strongly [that] in the end, all life is on the record," Smith says—"you should stand by what you say, and you should put your own name on it. It makes me uncomfortable that science has moved away from that."
"I believe strongly [that] in the end, all life is on the record," Smith says—"you should stand by what you say, and you should put your own name on it. It makes me uncomfortable that science has moved away from that."


*[http://www.edge.org/3rd_culture/kelly06/kelly06_index.html SPECULATIONS ON THE FUTURE OF SCIENCE] By Kevin Kelly : "Wikiscience" is leading to perpetually refined papers with a thousand authors.  Distributed instrumentation and experiment, thanks to miniscule transaction cost, will yield smart-mob, hive-mind science operating "fast, cheap, & out of control."  Negative results will have positive value (there is already a "Journal of Negative Results in Biomedicine"). Triple-blind experiments will emerge through massive non-invasive statistical data collection--- no one, not the subjects or the experimenters, will realize an experiment was going on until later. (In the Q&A, one questioner predicted the coming of the zero-author paper, generated wholly by computers.)"
*[http://www.edge.org/3rd_culture/kelly06/kelly06_index.html Speculations on the future of science] By Kevin Kelly : New ways of knowing will emerge.  "Wikiscience" is leading to perpetually refined papers with a thousand authors.  Distributed instrumentation and experiment, thanks to miniscule transaction cost, will yield smart-mob, hive-mind science operating "fast, cheap, & out of control."  Negative results will have positive value (there is already a "Journal of Negative Results in Biomedicine"). Triple-blind experiments will emerge through massive non-invasive statistical data collection--- no one, not the subjects or the experimenters, will realize an experiment was going on until later. (In the Q&A, one questioner predicted the coming of the zero-author paper, generated wholly by computers.)"
:"Wiki-Science – The average number of authors per paper continues to rise. With massive collaborations, the numbers will boom. Experiments involving thousands of investigators collaborating on a "paper" will commonplace. The paper is ongoing, and never finished. It becomes a trail of edits and experiments posted in real time — an ever evolving "document." Contributions are not assigned. Tools for tracking credit and contributions will be vital. Responsibilities for errors will be hard to pin down. Wiki-science will often be the first word on a new area. Some researchers will specialize in refining ideas first proposed by wiki-science. "
 
Automated contributions:
*[http://dx.doi.org/10.1126/science.1165893 Distilling Free-Form Natural Laws from Experimental Data]
*[http://dx.doi.org/10.1126/science.1165620 Automated hypothesis generation and testing], even [http://dx.doi.org/10.1126/scitranslmed.3000390 high throughput] and [http://dx.doi.org/10.1126/science.1189416 across domains]
*Bot-assisted integration of knowledge manually curated in different environments (e.g. [http://en.wikipedia.org/wiki/Portal:Gene_Wiki GeneWiki] and [http://www.wikigenes.org WikiGenes])
*[http://www.edge.org/3rd_culture/kelly06/kelly06_index.html Zero-author papers]
 
[http://www.eastbayexpress.com/gyrobase/publisher-for-the-people/Content?oid=1075372&showFullText=true Publisher for the People] (see also [http://ff.im/p62G2 this FriendFeed thread])
"The goal of research is to improve our knowledge. It's a cumulative process in which discovery begets discovery as scientists build on the work of their predecessors. But to unravel the mysteries of life and the cosmos, researchers need access to all available information, and that means journals, the main medium by which scientists communicate. By limiting public access now that electronic distribution is available, the journal industry is effectively working against the larger goals of science."


From [http://www.edge.org/3rd_culture/kelly06/kelly06_index.html Speculations on the future of science]:
----
“if you publish in a journal which charges for access, you are not published, you are privated. Published means to make public. If the public does not have access to it except for by a fee, it is not public, it is private.” ([http://www.christopherdickman.org/archives/15 Dave Parry])
----
[[User:Daniel Mietchen/Talks/Integrating wikis with scientific workflows/Introduction]]


*"Wiki-Science – The average number of authors per paper continues to rise. With massive collaborations, the numbers will boom. Experiments involving thousands of investigators collaborating on a "paper" will commonplace. The paper is ongoing, and never finished. It becomes a trail of edits and experiments posted in real time — an ever evolving "document." Contributions are not assigned. Tools for tracking credit and contributions will be vital. Responsibilities for errors will be hard to pin down. Wiki-science will often be the first word on a new area. Some researchers will specialize in refining ideas first proposed by wiki-science. "


*"New ways of knowing will emerge. "Wikiscience" is leading to perpetually refined papers with a thousand authors. Distributed instrumentation and experiment, thanks to miniscule transaction cost, will yield smart-mob, hive-mind science operating "fast, cheap, & out of control." Negative results will have positive value (there is already a "Journal of Negative Results in Biomedicine"). Triple-blind experiments will emerge through massive non-invasive statistical data collection--- no one, not the subjects or the experimenters, will realize an experiment was going on until later. (In the Q&A, one questioner predicted the coming of the zero-author paper, generated wholly by computers.)"
 
==Notes==
*use screenshots of Recent changes from mainspace around midnight from WP, EoE, SP, CZ, WE & OWW & Knol
----
*Mention possibility of linking to Open Access funding, as per [http://ff.im/oyzlk Microfinancing for science]
----
*[http://project.liquidpub.org/ Liquid Publications] — the editable web
----
On the cover image: Journals are not essential to a wiki system described here, as their function of conveying new information would go away, but they still have their role in turning edit histories into stories, and in framing debates, for which wiki talk pages are not ideal.
----
Numbered referencing (as in [[Gyrification]]), or Harvard style (e.g. [[Brain morphometry]]).
:Link to [http://acawiki.org/ AcaWiki]
:Mention interwiki links
----
*[http://www.nettab.org/2010/progr.html Conference on Bio wikis]
----
*Retractions: [http://scienceblogs.com/pharyngula/2010/08/another_publisher_stonewalls_o.php perspective];  [http://www.rin.ac.uk/node/653 "retractions at Wiley-Blackwell are now running at more than one a week"]; see also [http://en.wikiversity.org/wiki/Wikis_in_scholarly_communication#Comparison_between_paper-based_and_wiki-based_scholarly_communication_systems Comparison between paper-based and wiki-based scholarly communication systems]
----
*[http://scholar.google.de/scholar?hl=en&q=%22magnetic+resonance+imaging+is+a%22&as_sdt=2000&as_ylo=2001&as_vis=0 articles in Google Scholar since 2001 that use the phrase "magnetic resonance imaging is a"]
*[http://scholar.google.de/scholar?hl=en&q=%22the+brain+is+a%22&btnG=Search&as_sdt=2000&as_ylo=2001&as_vis=0 articles in Google Scholar since 2001 that use the phrase "the brain is a"]
----
*[http://blog.openwetware.org/community/2009/07/25/referencing-a-doi-within-openwetware/ Referencing a DOI Within OpenWetWare]
----
*see also [[User:Daniel Mietchen/Talks/Integrating wikis with scientific workflows/Publishing/Parry's recommendations]]
----
*[http://lists.wikimedia.org/pipermail/foundation-l/2010-August/060306.html <nowiki>[</nowiki>Foundation-l<nowiki>]</nowiki> Call for Volunteers: Wikimedia Research Committee]
----
#REDIRECT [[User:Daniel_Mietchen/Talks/COASP_2010/Start]]

Latest revision as of 03:41, 22 November 2023


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Session start · Talk start · Quotes · Background · Wikis as science communication platforms ·
Wikis as platforms for Open Access publishing · Prototypes · Editorial policies · Guided tour ·
Obstacles · Alternatives · Outlook · Summary · Slides · Video · Q & A · Demo

This page hosts supplementary notes for a talk in the Session on Editorial Innovation in OA Publishing at COASP, August 23, 2010, Prague. I hope it will be useful during the Q & A session and for later reuse.


Wikis as platforms for scholarly publishing

Functions of scholarly publishing

See also this Friendfeed thread.

  • Inform about new knowledge
  • Archive existing knowledge
  • (Make profit)

More detailed listings

Just for reference

  • Essential elements of science publishing:
    • Research
    • Documentation
    • Making things public
    • Integration with previous and future knowledge
    • Discussion
  1. importance,
  2. usefulness,
  3. relevance,
  4. methodology,
  5. ethics,
  6. completeness
  7. accuracy of an article
  8. accountability (added by Peter Frishauf in part 4)
  1. "Selection: it has been said that publishers are better defined by what they do not publish rather than by what they do. A key part of what publishers do lies in the editorial process--selection, acquisition, commissioning."
  2. "Finance: publishers take the--sometimes considerable--financial risk in publishing, and can reasonably expect to make a return broadly commensurate with that risk."
  3. "Organization: at the core of the publisher's role is the co-ordination of all the developmental processes that turn the author's raw material into a finished product for the market. This is an often-overlooked part of the publisher's art. It perhaps becomes most obvious only by its absence."
  4. "Aggregation: it may seem odd to talk about aggregation as being part of a traditional publisher's role, but we would argue that there is nothing new about aggregation of content. The book and journal publishing supply chains are focused on aggregating the works of individual authors--with the ultimate aggregators in the physical world being bookstores and libraries. It is typically to these points of aggregation that consumers go to purchase or borrow the particular item to which they want access."
  5. "Marketing: last, perhaps, but certainly not least. Marketing is selfevidently a crucial element of the publisher's role. Here, we mean marketing in its broadest sense ensuring that products are appropriate to the markets for which they are published as well as promoting the products to the markets themselves. In this context, we see marketing as including both customer service and distribution channel management."



Quality assessment

Traditionally

Single-blind or double-blind or open peer review, with the reviewers or even authors always or optionally, temporarily or permanently remaining anonymous, with simple accept/ revise/ reject decisions or interactive two-stage or multi-stage discussions, in public or hidden from it (possibly even in part), before and/ or after formal publication.

Some non-wiki examples:

  1. Copernicus journals
  2. PLoS journals
  3. Frontiers journals
  4. BMC journals
  5. Semantic Web journal
  6. Rejecta Mathematics
  7. WebMedCentral
  1. Reviewers are biased by personal motives
  2. Peer review is too slow, affecting public health, grants, and credit for ideas
  3. Too many papers to review
  • Respective solutions:
  1. Eliminate anonymous peer review ( Biology Direct, BMJ, BMC); run open peer review alongside traditional review (Atmospheric Chemistry and Physics); judge a paper based only on scientific soundness, not impact or scope (PLoS ONE)
  2. Shorten publication time to a few days (PLoS Currents Influenza); bypass subsequent reviews (Journal of Biology); publish first drafts (European Geosciences Union journals)
  3. Recycle reviews from journals that have rejected the manuscript (Neuroscience Peer Review Consortium); wait for volunteers (Chemical Physics Letters); reward reviewer efforts (Biology Direct, BMC, Frontiers, ACP)
P ≠ NP and the future of peer review
Rethinking Peer Review As The World Peer Reviews Claimed Proof That P≠NP
"Apparently, people are realizing that a much more open post-publication peer review process, where anyone can take part, is a lot more effective"
"we have very little evidence that pre-publication closed peer review is any good at any of these things. In a sense, as scientists this should be obvious. You would never make a strong claim based on a very small number of measurements, which rarely come to the same result, and then hide the actual data away where no-one can see it. Yet this is exactly what we do with pre-publication peer review in most cases."

On wiki

In principle, any system of (peer) review can be implemented on a wiki, by detailed management of user rights: The usual

Some wiki examples:

  1. English Wikipedia (Flagged Revisions, WikiTrust, Wikipedia:Pending changes)
  2. Scholarpedia
  3. Encyclopedia of Earth
  4. Citizendium



Business models

  • Main ones: author-pays, (partial) subscription, philanthropy, advertising, premium services
  • Micropayments Science-specific/ general?

Opportunities

PD Image
Search by license — not possible yet. Why?
Non-wiki example
MediaWiki as a blog, using Semantic MediaWiki
Also for references

Quotes

From the JoPM peer review discussion (my comments)

Peter Frishauf, founder of Medscape (3:29-3:44 in part 4):"Wikipedia is probably the most robust Petri dish we have for actually studying the process of words and contributions, because it is auditable."

Elizabeth Wager of Jefferson et al., 2002 (10:37-10:56 in part 4): "So, we had the idea that you do your systematic review before you do your research; you do your research, and then if you haven't changed much, you haven't really made a big impact, whereas if you've actually shifted things one way or the other and made it more precise then you have."

Peter Sefton (The next wave in scholarly word processors?): "what I think we need in scholarship is the web, but editable"

Chris Gutteridge (in 1st comment on Sefton's post): "Better still, if you assert something said in another paper, sod the citation, transclude the relevant text, with a full electronic citation allowing you to verify it."


From I Hate Your Paper - The Scientist "I believe strongly [that] in the end, all life is on the record," Smith says—"you should stand by what you say, and you should put your own name on it. It makes me uncomfortable that science has moved away from that."

  • Speculations on the future of science By Kevin Kelly : New ways of knowing will emerge. "Wikiscience" is leading to perpetually refined papers with a thousand authors. Distributed instrumentation and experiment, thanks to miniscule transaction cost, will yield smart-mob, hive-mind science operating "fast, cheap, & out of control." Negative results will have positive value (there is already a "Journal of Negative Results in Biomedicine"). Triple-blind experiments will emerge through massive non-invasive statistical data collection--- no one, not the subjects or the experimenters, will realize an experiment was going on until later. (In the Q&A, one questioner predicted the coming of the zero-author paper, generated wholly by computers.)"
"Wiki-Science – The average number of authors per paper continues to rise. With massive collaborations, the numbers will boom. Experiments involving thousands of investigators collaborating on a "paper" will commonplace. The paper is ongoing, and never finished. It becomes a trail of edits and experiments posted in real time — an ever evolving "document." Contributions are not assigned. Tools for tracking credit and contributions will be vital. Responsibilities for errors will be hard to pin down. Wiki-science will often be the first word on a new area. Some researchers will specialize in refining ideas first proposed by wiki-science. "

Automated contributions:

Publisher for the People (see also this FriendFeed thread) "The goal of research is to improve our knowledge. It's a cumulative process in which discovery begets discovery as scientists build on the work of their predecessors. But to unravel the mysteries of life and the cosmos, researchers need access to all available information, and that means journals, the main medium by which scientists communicate. By limiting public access now that electronic distribution is available, the journal industry is effectively working against the larger goals of science."


“if you publish in a journal which charges for access, you are not published, you are privated. Published means to make public. If the public does not have access to it except for by a fee, it is not public, it is private.” (Dave Parry)


User:Daniel Mietchen/Talks/Integrating wikis with scientific workflows/Introduction


Notes

  • use screenshots of Recent changes from mainspace around midnight from WP, EoE, SP, CZ, WE & OWW & Knol



On the cover image: Journals are not essential to a wiki system described here, as their function of conveying new information would go away, but they still have their role in turning edit histories into stories, and in framing debates, for which wiki talk pages are not ideal.


Numbered referencing (as in Gyrification), or Harvard style (e.g. Brain morphometry).

Link to AcaWiki
Mention interwiki links







  1. REDIRECT User:Daniel_Mietchen/Talks/COASP_2010/Start