Talk:WikiJournal/Archive 1

Interesting idea

(I should declare an interest: I an a trustee of a learned society which publishes conventional and open-access journals).

This is a very interesting suggestion, and worth considering. Sir Timothy Gowers has been promoting a not dissimilar project, see for example here. Among the questions that occur to me – Should the project partner with one or more existing non-proft publishers and/or existing open access journals? Is open discussion on published papers allowed? Should it be moderated and if so by whom? Are updated papers which have been peer-reviewed a second time to be regarded as the same paper, a new version or a completely novel publication? Would the project adhere to the Vancouver Declaration and if so how would that be managed? Who selects the peer reviewers? Are they rewarded and what mechanisms exist to ensure that they carry out their reviews in a timely and proper manner? What precautions, if any, should be taken to prevent abuse of the refereeing or citations? Overall, what resources would be required to sustain publication? Rogol Domedonfors (talk) 20:31, 16 September 2016 (UTC)

Some followup suggestions. Is the WikiJournal intended to attract high-quality scientific research papers in competition with existing journals with high impact factors that make them attractive for potential authors? If so, you may need to scale back you ambitions, at least initially. Is it intended for surveys or conference proceedings? What is its relationship with the ArXiv? How does it fit into the Open Access publishing models which are becoming mandatory for recipients of a wide range of research grants? What is the proposal for handling associated intellectual property rights, such as patents? Will there be an associated repository for code and data, and if so, what are the access rights ans requirements around those? Rogol Domedonfors (talk) 20:17, 17 September 2016 (UTC)

Many question, but I will try to answer them.Mikael Häggström (talk) 20:09, 18 September 2016 (UTC)

• Should the project partner with one or more existing non-proft publishers and/or existing open access journals?

I definitely think so. It is on the to-do list to come in contact with related projects such as Academia.wikia.com and OpenMedicine.ca.Mikael Häggström (talk) 20:09, 18 September 2016 (UTC)

• Is open discussion on published papers allowed? Should it be moderated and if so by whom?

Yes, they can be discussed at their talk pages, without moderation. Changes can be proposed, and if it alters the meaning of the work it may undergo renewed peer review and author approval, and then come live.Mikael Häggström (talk) 20:09, 18 September 2016 (UTC)

• Are updated papers which have been peer-reviewed a second time to be regarded as the same paper, a new version or a completely novel publication?

It would become a new version. All previous versions can easily be viewed in the history tab.Mikael Häggström (talk) 20:09, 18 September 2016 (UTC)

• Would the project adhere to the Vancouver Declaration and if so how would that be managed?

The journal does not adhere to particulars of the Vancouver protocol (such as "Double space all parts of manuscripts") but adheres to the more general ICMJE recommendations mentioned therein. Mikael Häggström (talk) 20:09, 18 September 2016 (UTC)

• Who selects the peer reviewers?

The editorial board. Mikael Häggström (talk) 20:09, 18 September 2016 (UTC)

• Are they rewarded and what mechanisms exist to ensure that they carry out their reviews in a timely and proper manner?

Peer reviewing is performed on a volunteer basis. The peer review guidelines state that "Initial peer reviews should preferably be written within 3 weeks", and if they don't meet this deadline they will get reminders. In worst case, the task may be transferred to someone else. Mikael Häggström (talk) 20:09, 18 September 2016 (UTC)

• What precautions, if any, should be taken to prevent abuse of the refereeing or citations?

If you mentioned examples of how such abuse could manifest, I could answer more clearly. Mikael Häggström (talk) 20:09, 18 September 2016 (UTC)

• Overall, what resources would be required to sustain publication?

The minimal requirement is currently $291 annually (for Crossref membership, and for the www.wijoumed.org domain), and is in need of this funding from Wikimedia so that we don't have a conflict of interest by funding the initiative ourselves. After all, it is not a large sum. Mikael Häggström (talk) 20:09, 18 September 2016 (UTC)

• Is the WikiJournal intended to attract high-quality scientific research papers in competition with existing journals with high impact factors that make them attractive for potential authors?

Yes, but not exclusively. Mikael Häggström (talk) 19:22, 9 October 2016 (UTC)

• Is it intended for surveys or conference proceedings?

Possibly surveys if they are in an article format. Mikael Häggström (talk) 19:22, 9 October 2016 (UTC)

• What is its relationship with the ArXiv?

Currently none. Mikael Häggström (talk) 19:22, 9 October 2016 (UTC)

• How does it fit into the Open Access publishing models which are becoming mandatory for recipients of a wide range of research grants?

It is open access, and I believe that fits best for all grant recipients. Mikael Häggström (talk) 04:49, 23 September 2016 (UTC)

• What is the proposal for handling associated intellectual property rights, such as patents?

Authors need to include a submission letter, where they need to explain any conflicts of interests relating to patents. Mikael Häggström (talk) 20:07, 9 October 2016 (UTC)

• Will there be an associated repository for code and data, and if so, what are the access rights ans requirements around those?

Authors are encouraged to upload code and data as well to be open-access. We do have a file repository where they can be uploaded and linked from articles. Mikael Häggström (talk) 19:22, 9 October 2016 (UTC)

Inviting you to participate in the women editing contest "The women you have never met"

Dear WikiJournal!

Hope this message finds you all well :) On behalf of Iberocoop network I want to invite you to be part of the women editing contest we are organizing along with many other chapters and user groups in the movement. You are doing an excellent work on your local context and we will be so pleased to have you on board. In this very early stage, we are asking the organizations to add their interest in the following meta page Hope to see you there soon! Hugs----Anna Torres (WMAR) --Anna Torres (WMAR) (talk) 15:31, 25 January 2018 (UTC)

Epub as export format

PDF is common now, but I believe EPUB is a way better format for device independent publishing. — Jeblad 18:44, 3 June 2019 (UTC)

• EPUB is not an open format. —Justin (koavf)❤T☮C☺M☯ 02:59, 5 June 2019 (UTC) Don't listen to me: I'm an idiot. —Justin (koavf)❤T☮C☺M☯ 16:38, 6 June 2019 (UTC)
  • I believe this must be a misunderstanding. A standard body may publish standards documents with a non-free license, but using facts from the same documents will be free anyhow. Packing a pub-file according to those facts will be free. I can't find any doc from ISO saying otherwise, but feel free to post links! Also the IDPF is a working group under W3, with a W3C Community Final Specification Agreement. In particular note: I grant to you a perpetual (for the duration of the applicable copyright), worldwide, non-exclusive, no-charge, royalty-free, copyright license, without any obligation for accounting to me, to reproduce, prepare derivative works of, publicly display, publicly perform, sublicense, distribute, and implement the Specification to the full extent of my copyright interest in the Specification. This is defacto a CC-by type of license. I believe we can use this standard. — Jeblad 14:28, 6 June 2019 (UTC)
    • I don't think we should export files that cannot be uploaded to c:, so exporting EPUB should be contingent on phab:T19858. —Justin (koavf)❤T☮C☺M☯ 16:38, 6 June 2019 (UTC)
      • It's great to have your technical feedback on the proposal, I must admit, I don't know much about the details of the EPUB format. T.Shafee(Evo﹠Evo)^talk 14:57, 7 June 2019 (UTC)
        • The problem is that with many EPUBs, the image quality is oftentimes bad. Plus, the user will need a dedicated EPUB format. PDF is the most widely used publishing format, and most people are conventient with, and know how to open, read as well as use features such as add annotate and highlight text. Br shadow (talk) 17:21, 11 July 2019 (UTC)
          • Overall, I think that PDF is the necessity, with epub as a useful addition to be future-ready if implementation is not too difficult. A major bottleneck is that currently the PDFs are manually typeset in a MSword template. T.Shafee(Evo﹠Evo)^talk 23:24, 11 July 2019 (UTC)

Duplicate project?

I wonder if WikiJournal is Wikiversity, but a specific aspect of it. Perhaps only me that fails to see the motivation of a separate project. — Jeblad 18:46, 3 June 2019 (UTC)

My perspective is that overall it has a different remit to wikiversity (individual journal articles, rather than whole modules or university courses) and has some different technical requirements (peer review policies, metadata readability for indexing services, default cc-by licenses), and some different layout requirements (e.g. for ease of site navigability). T.Shafee(Evo﹠Evo)^talk 14:55, 7 June 2019 (UTC)

Fonts

The item “Specific title fonts” is, well, to specific. This is part of the styling for the skin, and should not be changed. — Jeblad 18:51, 3 June 2019 (UTC)

Yes, this point was a little over-specific. In general, it meant support for a different set of css and standard templates inserted based on namespace (e.g. this template is included in every article and preprint and peer review page, this template is included on description pages, this template is used on long pages, and this template is used to default format figures). It might be worth changing the wording on the proposal page to be clearer. T.Shafee(Evo﹠Evo)^talk 13:37, 7 June 2019 (UTC)

Note that a process can be implemented by moving pages between namespaces, and specific namespaces can then be given its own header and footer. If there are a lot of hidden maintenance stuff that should not be part of the template, like whether a page should be indexed, this can be an efficient and user friendly solution. — Jeblad 12:50, 10 June 2019 (UTC)

Lock down editing and view

Some articles must be locked for editing by anyone outside a limited author group. (Make it possible to use published articles as part of a degree.) This group will have no special rights outside the specific article. Members of this group may also be the only ones being able to view the pages content, except for users with elevated rights. (Make publishing outside WikiJournal possible.) — Jeblad 19:01, 3 June 2019 (UTC)

There are probably two (three?) different edit situations. One where you have a locked group where others can't join as authors even if they want to, even if they are fully qualified, and even if the users in the group want to invite them. That is authorship of articles being part of some graded work. Then you have semi open groups where authors in the group can invite external users. That is authorship of articles that is not part of graded work, but where some publisher has specific demands about authorship. Then you have fully open articles, like in Wikipedia. — Jeblad 14:54, 6 June 2019 (UTC)

User groups

The statement “specialized logins as authors, editors and/or peer reviewers” is probably wrong. User login is similar, but they are assigned to different groups. Also “one individual having multiple capacities” can be handled as a merger of rights from different groups. The statement “on-wiki storage of confidential information” is an user allowed to hide a page from common view, but I wonder if this is really about a user being able to use a cloaking identifier for a specific page.

Note that elevated access rights limited to a group of pages is the opposite of phab:T2674. — Jeblad 19:03, 3 June 2019 (UTC)

Legal name

This one “Specification of legal name and contact details might be required.” I can't imagine a situation where a scolarly publication can be acceptable without correct legal name? Any example? — Jeblad 19:42, 3 June 2019 (UTC)

There is some precedent for anonymous and pseudonymous authors in certain circumstances (Pubmed articles with [AUTHOR]="Anonymous" include the BMJ). It is certainly possible to attribute anonymous/pseudonymous contributors (who do not need to meet ICMJE author guidelines) - for example doi:10.15347/wjs/2018.006. For actual corresponding/submitting authors, journals usually only publish anonymously for specific reasons (e.g. safety or risk to author). Although there are a number of editorials about the practice, I've not found any published guidelines for recommended practice/implementation. Obviously the icmje guidelines state "Agreement to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved". This is usually interpreted to mean open identity, affiliation, and contact information, however I suspect that a standard could be developed for how to satisfy the requirements with an anonymous author when necessary (e.g. confidential identity known to the journal, cryptographic key provided to the author, contact form/email to reach author without revealing identity). T.Shafee(Evo﹠Evo)^talk 14:04, 7 June 2019 (UTC)

I guess this will very quickly turn into a discussion about authentication, authorization, and identity. You can authorize an account to do some operations, and that account can authenticate itself, but that does not imply it is identified. Previously I have proposed we should use w:Security Assertion Markup Language as that would provide access to w:no:FEIDE which is the common w:identity management system for schools and universities in Norway. FEIDE has also made a small implementation of a SAML service, and that could be used by local WMF affiliates to provide identity federation. It is also possible to piggyback identity on VISA payments and payments by other such systems, although I'm not sure this works for all types of payment. Still note that in some countries ownership of an account is a pretty weak indication of an identity. — Jeblad 18:54, 10 June 2019 (UTC)

Permalink

I wonder if it would be a good idea to surface a permalink to the article as such, and not just the revision as we do it now. This would be stable during move actions, and also during article updates. Not sure whether it would be difficult for users to have two different permalinks, one for the revision and one for the article. A doi would be a permalink from an external entity, and would be assigned after “publication”. — Jeblad 20:03, 3 June 2019 (UTC)

That could be an interesting idea. In generally there are a few tools around permalinks that will be very useful (e.g. the ability to state an page and a date and see the article as it existed then without having to know the oldid number (also very useful to automatically linking to how the article looked when a peer reviewer comments were made (currently handled manual via this template). T.Shafee(Evo﹠Evo)^talk 13:44, 7 June 2019 (UTC)

A function to subst the subject pages revision id as it was when the template was added? The special page is mw:Help:PermanentLink, so should be something like [[Special:PermanentLink/{{subst:{{REVISIONID:{{SUBJECTSPACE}}:{{PAGENAMEE}}}}}}]]. Seems like this have to use a wrapper template. — Jeblad 14:29, 10 June 2019 (UTC)

Yes, although supplying a date rather than a REVISIONID will be much more user-friendly (even if there's just some simple tool that calculates the REVISIONID from a date so that we don't need to use the sub-optimal https://en.wikiversity.org/w/index.php?title={{ARTICLEPAGENAMEE}}&action=history&limit=1&offset={{Date|{{{date}}}|ISO}}! T.Shafee(Evo﹠Evo)^talk 05:41, 17 June 2019 (UTC)

Front matter

This is about the statement “synchronisation of article info template on main and talk pages” and “of the tracking sheets when reviewer comments submitted”, and partly about “metadata-submission to crossref of accepted articles” and “XML annotation of articles in the JATS format”. The later two are about exporting metadata.

Not sure what would be best; front matter as in Jekyll, it could be on a subpage, or structured data as it is used on c:Commons:Structured data. The articles will be nearly the same as media files, so it should be quite easy to adapt the existing extension. — Jeblad 14:58, 6 June 2019 (UTC)

Hidden contribution

If hidden contributions should be allowed, that is you author an article without public view or you peer review an article, then that is an functionality for identified users only. If anonymous users are allowed to make hidden contributions it would create a horrible situations for those fighting vandalism. I can't really see anonymous users being allowed to contribute anywhere except on talk pages on this kind of wiki, at least they can't contribute on an article with a closed or semi closed author group. — Jeblad 15:11, 6 June 2019 (UTC)

Yes, I agree, it wouldn't be hidden as such, it'd just be a way of linking an identity to a username when necessary. Currently this is via off-wiki steps. For example, peer reviews are submitted via this google form, which deposits them to a google spreadsheet like this, where they're copied to the relevant article talkpage, and noted down on this tracking table, and maybe at some point will have their metadata added to Wikidata. technical solutions could simplify, automate, and ideally avoid the need for third-party platforms to keep the records. T.Shafee(Evo﹠Evo)^talk 14:09, 7 June 2019 (UTC)

As an additional note, it is standard for there to be hidden information within wikis (e.g. Special:AbuseFilter, Special:Undelete) and several key wiki processes simply keep confidential information off-wiki in mailing lists (e.g ArbCom, OTRS). T.Shafee(Evo﹠Evo)^talk 13:12, 8 June 2019 (UTC)

Of course there are some case where there must be restricted acces. But I know no Wikimedia project, where there is restricted, and by this intransparent, acces for normal content-related work. And it is an founding principles for all Wikimedia projects that all must be able to involve. Habitator terrae (talk) 14:17, 8 June 2019 (UTC)

I think it would actually be quite viable to drop the option for "certain pages not being publicly accessible such that press embargo for unpublished articles" from the Technical requirements list. It was added early in the proposal during 2016, only one author has taken the journals up on that possibility, and the explosion in preprint server usage has meant that now essentially all journal publishers now accept works from preprints. I'd therefore happily see it stricken from the requirements list. T.Shafee(Evo﹠Evo)^talk 04:42, 9 June 2019 (UTC)

There is no system that is perfect. Even OTRS-wiki had leaked information in the past. OhanaUnited^{Talk page} 21:29, 9 June 2019 (UTC)

Foundation wiki has restrictions, OTRS wiki has restrictions, and there are probably more. I can't really see problems with having restrictions, except it must be limited to a specific group with additional rights. Also hidden contributions in this case will not follow group rights but contributor rights. — Jeblad 14:39, 10 June 2019 (UTC)

First: The Foundation wiki is not a Wikimedia Project, as defined in der founding principles @Jeblad: The Foundation wiki is for organisation, the OTRS wiki for verification, but both are not for content creation, which was until now a full transparent work. Habitator terrae (talk) 19:14, 11 June 2019 (UTC)

I disagree, but I also believe this part of the thread has lost track. — Jeblad 20:51, 11 June 2019 (UTC)

This is becoming less and less like a Wiki. * Pppery * _{has returned} 14:10, 8 June 2019 (UTC)

Wikis in general are a wide concept, but this type of project is probably best geared for a different wiki software that is much more compatible with much more hierarchical permissions organization (i.e. not Mediawiki). No water off my back though if you manage to coax Wikimedia developers into creating additional features for all this. --Tropylium (talk) 17:27, 8 June 2019 (UTC)

I doubt that the WMF board will approve any sister project not based on MediaWiki. * Pppery * _{has returned} 01:06, 9 June 2019 (UTC)

Well, unless it was like Wikidata and super heavily modified (in that case by leaning on Wikibase), but I doubt that is what Tropylium actually meant. I agree though; it'd tank this proposal. –MJL ‐Talk‐^☖ 02:08, 9 June 2019 (UTC)

Wikibase is nothing more than a complicated MediaWiki extension. As I pointed out in my initial oppose to the proposal, keeping some Wiki pages hidden from the public is something that MediaWiki.org claims cannot be done securely. * Pppery * _{has returned} 15:57, 9 June 2019 (UTC)

There are many years since the right to read was added to the Mediawiki software. At Wikipedia even anonymous users has this right, that is why you does not have to log in. — Jeblad 14:42, 10 June 2019 (UTC)

Comments and queries

Sorry, I haven't spent much time reading the proposal in detail, and I'm unfamiliar with the existing three journals. But I do have extensive experience in helping researchers to publish in journals and elsewhere.

I'm very keen to see more open-source academic outlets; but I must stress that unless they are (or become) desirable targets for researchers to publish in (through impact factors, etc), it would be hard-going.

• (1) How would this arrangement differ from those of traditional online, open-source journals? If I recall from the proposal text, edits would be allowed after publication, too. I don't see how this could work, or how it wouldn't vastly reduce the status of the journals.

• (2) Editing a "manuscript" in public would be rather difficult. I think that wouldn't gain acceptance by the academic establishment, because it would undermine the whole notion of authorship. Academics need to gain career capital from their publications: that is critical.

• (3) I do see a great opportunity in having talkpages for comments and feedback after publication – that is totally absent from academic journals at the moment, even those that are solely online. There would need to be protocols, and someone to police them.

Tony (talk) 10:45, 7 June 2019 (UTC)

Thanks for applying your research consultant experience to the workings of the proposal. My hope is that individual journals should be able to function at a variety from scales (from 10 publications per year upwards). I think that they can be come desirable targets for a few reasons (more in below sections #Why_would_an_academic_choose_a_WikiJournal and #Impact_and_reach). The limiting factor on submissions, I think, has more been visability and publicity.

• re 1a) A Mediawiki platform provides a few differences to existing OA journals. One is the ease of wikimedia-integration (into wikipedia, commons, wikiversity, wikibooks etc). Another is that it can be done free of article processing charges.
• re 1b) The doi-linked, stable, version of record would be set aside. So far we kept any post-publication edits to being minor copyedits, and formatting. At the moment, there is no locking of any sort. However, it's noted that once an article is assigned a doi, that meaning-changing edits would be re-peer-reviewed and an updated doi minted by from crossref's crossmark service along the lines of this article. Copyedits and formatting are always fine though. So far, the vast majority of editing has occurred before the doi assignment, and articles integrated into Wikipedia have a note in the top right to let people know that they can more logically be edited there (example).
• re 2) There's a certain precedent from the increasing use of preprint servers, but you're right that doing the whole editing process publically could be a turn-off. Nevertheless that's not actually something we've had any negative feedback on so far as I know.
• re 3) Yes, post-publication peer review will be valuable. Where content is integrated into other wikimedia projects conversation can also bee directed towards thee relevant talkpages there. The wikimedia ecosystem already has good experience on talkpage dynamics and we will also have to learn from the experiences of PMC [1] [2] and others.

T.Shafee(Evo﹠Evo)^talk 14:49, 7 June 2019 (UTC)

On 1b: All post-publication edits must be accepted by all major authors, as it must be them that initiates a re-peer-review. Except for proofreading and copyediting there should be no substantial changes to a published paper. (That is not “copyediting” as done on Wikipedia, some users completely rewrite articles and claim it is only copyediting.) — Jeblad 16:47, 10 June 2019 (UTC)

• Thanks for your responses, Evo and Jeblad. 1b is a sticking point. When researchers cite another work, they won't be happy knowing that it might change later. I can't see their journal editors being happy either, or their readers. One solution is to make the doi version the only one that is up for citation; but it rather defeats the purpose of post-publication editing. In my view, to gain any credibility in the research world, the publication must stay fixed, as everywhere else. There should not be typos in it, and it should have been properly copy-edited. Tony (talk) 10:11, 12 June 2019 (UTC)

Using versioning for papers is nothing new, see for example this paper; The Tsetlin Machine - A Game Theoretic Bandit Driven Approach to Optimal Pattern Recognition with Propositional Logic [3]. As of this writing it has 11 versions. — Jeblad 15:36, 12 June 2019 (UTC)

So if I want to direct-quote text from one of those papers, I can do it in a way that links the reader to those exact words, even if they've subsequently been edited? How? Tony (talk) 04:46, 13 June 2019 (UTC)

Link to version 6: https://arxiv.org/abs/1804.01508v6 (https://arxiv.org/pdf/1804.01508v6.pdf), link to version 9: https://arxiv.org/abs/1804.01508v9 (https://arxiv.org/pdf/1804.01508v9.pdf). Note the version suffix. You can link to pages inside a pdf, with some variations given the software you use. This example should probably work for all https://arxiv.org/pdf/1804.01508v9.pdf#page=3. You can not in general link to phrases inside a pdf, but you can link to prepared anchors. On a wikipage (htmlpage) it is possible to point to a specific phrase with some additional code (see #Pointing to specific parts of a page). [I should have added that this is randomly chosen versions, and not the final ones.] — Jeblad 12:37, 13 June 2019 (UTC)

I'm glad to know this. As long as users know it. It does bother me that there's no dedication to a "final" version. That's what the research world is used to. If it's wrong, you publish another article. And if the wording sucks, well, we're used to that, mostly in B-grade journals, though occasionally in the top-tier journals. Maybe it would work.

More generally, success of this proposal becomes a question of credibility in a highly competitive environment. There's little use in good running a whole bunch of journals that researchers (AND credible peer-reviewers) avoid, because their track-record needs high-profile publications. As a strategic adviser to researchers, I wouldn't like to see much wikijournal in their list of publications ... at least not at the moment. Because I have their career interest at heart.

I really, really want to see the power of the big-profit capitalist publishers like Elsevier and Springer BROKEN. The best way is to aim high with strict rules from the start. Tony (talk) 11:35, 14 June 2019 (UTC)

I agree. The version as linked to by the DOI should be stable and other versions should be linked to as unreviewed preprints, then if peer reviewed, listed as updated versions with new dois. I'd love to see long-term versioning of articles similar to textbooks. Indeed many review articles are effectively this but have to have different titles (e.g. cyclotides as drugs in 2002, 2006, 2009, 2012, 2013, 2017 ...). Other journals have experimented with 'living systematic reviews', and I think this platform could be ideal for it. T.Shafee(Evo﹠Evo)^talk 13:13, 14 June 2019 (UTC)

A live article can have its own doi, at least I can't see any problem with that. Perhaps something I'm missing. It would although be nice if we could link to specific phrases for specific versions, and compare that to the live version. — Jeblad 15:15, 15 June 2019 (UTC)

Further comments. That's sounding more hopeful. If there's to be post-production fluidity, it should be tightly controlled or it could easily wreck any claim to academic authority, where the odds are stacked against low-IF journals, and high-IF journals become prestigious and influential. Nothing less would do, in my view, if wikijournals are to make a strong contribution to shifting the model of research publishing toward open scholarship and science. Note that it can take a few years to inch a publication into prestige, rather than falling into the bad end of a self-perpetuating inequality: low citation rates and therefore IF, difficulty of attracting good authors and peer-reviewers, returning full circle to continued low metrics.

So I wonder whether there's any chance that a "published" version would be created first up, with an unobtrusive link—perhaps above the abstract—to a list of linked updated versions, by date, with diffs and standard dispaly in separate links; it would be a great advantage if trivial edits did not claim their own version, but a group of admins were charged with deciding when an article had changed sufficiently for a new version-link. The simpler, the less cluttered, and the more like a traditional journal, the better.

Remember, I haven't had time to inspect the three existing wikijournals. Here are suggestions for kicking along impact factor, citations, and number of views.

• Organise a few authors (well in advance, please) to write review articles. These are magnets for citations. It's easier to attract a first author (who would themselves organise co-authors if necessary); and it's a particularly attractive to younger (postdoctoral fellow) authors, because the requirement for original data and concepts is much reduced or even eliminated, provided the article interprets progress in the field and outlines prospects for future progress. The occasional good review article (including one for the launching of the journal) would get the journal's name around.
• Have on-board a few good copyeditors (and why not name the assigned copyeditor succinctly at the end, as some online journals already do?). Don't rely on peer-reviewers for that: they should review a properly copyedited version. And I'm presuming there would be an "editor" (not a copyeditor) responsible for each article pre-publication.
• Display number of views at the end of the article.
• I presume there will be well-written and -designed instructions. Reference to external style guides is normal, if not essential, in instructions.

Tony (talk) 02:18, 15 June 2019 (UTC)

On the published articles: This can be handled by one or more of the main author(s) requesting a publication, while some other entity accepting the publication. In Norway we say that something is “tilgjengeliggjort” (“made available”) and then “publisert” (“made public”). In this context editing on-wiki only makes the new versions available, but for publishing we need something additional. Moving the article from a draft space (non-indexed) into a main space (indexed) could be this additional thing that makes the article published. For this change to take place the article should be peer reviewed, and I believe an article should have links to the peer reviews. This is rather easy to implement if we have a separate review-namespace. As the peer reviewers sort of grade the article, the authors should be able to grade the peer review. That gives an incitement to make good articles and good reviews.

On copyeditors: Listing copyeditors could be automated. An article has some official authors, but by measuring content change for each contributor other users than the authors could be found. Those could be listed as copyeditors. If the authors disagree with the copyeditors (they will) or other users find vandalism (they will) then a undo or rollback would be sufficient to remove them from the list of copyeditors. Editing with bots could be removed from the list of copyeditors if they are flagged as botusers. Copyeditors with to small contributions should probably be filtered out. Not sure what should happen if a copyeditor starts rewriting an article, it is quite common to dumb down articles at Wikipedia, often introducing factual errors in the process. Perhaps the only solution is a revert. — Jeblad 15:53, 15 June 2019 (UTC)

Thanks, some good points. As you probably guess, I favour a stricter rather than a looser procedure. In journal article preparation there's sometimes no clear boundary between scientific/scholastic authors, and copyeditors, since the former can conceivably do the latter (they should, frankly, especially if native-speakers of English, but standards are pretty bad). I'd prefer someone at Wikijournal (an admin or board member) to be officially in charge of each publication, from which time it would be given a status, from article creation onward, by that person. The status would progress in stages, by negotiation between the wikiperson in charge and the authors. The wikiperson would also recruit, say, a chief copyeditor to come in at stages agreed to by the main authors. Others could copyedit, but there would be someone ultimately responsible. This needs to be at a higher standard than English Wikipedia's pretty moribund featured article forum, where prose quality is very variable and is usually not sufficiently improved to call the product "professional". Wikijournals DO need to be professionally written, and that is hard (I find it hard myself). If Wikijournal is fussy (and helpful, too), it will earn respect among researchers. Tony (talk) 14:24, 16 June 2019 (UTC)

Being strict with the published versions will be important for satisfying their requirement as a Version of Record. We'l have to work out whether that's better technically handled by

1. adapting the versioning system in the history tab so that dois point to a specific REVISIONID (and also pointed to as the default when linking from e.g. an issue or the front page)
2. having the stable version at Journal/article (probably locked) and the editable version at Preprint/article (similar to the /sandbox subpage system used for updating high-use templates)

Currently I'd favour the second option as it's easier to implement, but the first may have more versatility long-term if tyhe interface could be made easier? The idea of better bring in copyeditors is also great. The project has so far been small enough that there have been few people stopping by to help out on that front (note at WP:OPYEDITORS), but that could certainly change. We've definitely had great interactions with COM:GL/I, sort of the images equivalent. The same may also be applicable to typesetting the final PDFs (though I'm helpful for greater automation assistance). T.Shafee(Evo﹠Evo)^talk 05:59, 17 June 2019 (UTC)

I would probably tag the published revisions, the rows in the history, and use a page specific right to limit who can change that tag. If you are an editor (not sure about your naming of the roles?) then you can change tags for a page where you are assigned editor rights.

The way Mediawiki works you should never be able to edit an old revision, all editing creates new revisions, thus pointing to a revision is safe and it will not change. With an exception if the page transcludes something, then that can change also for old revisions. For example Special:PermanentLink/15854603 points to an old version of the subject page. You can't edit this revision, all editing will create new revisions. By linking to a specific revision it is implicitly locked for further editing.

Note that linking to revisions are slow, and should probably be avoided in all cases except where a link to the revision is necessary. That is only linking from a box of published versions. All other linking should be to the current version.

DOIs should use oldid for the revision, but it could also be DOIs for curid or the article. The last one will always point to the current revision, but perhaps that should not exist outside WikiJournals? — Jeblad 11:28, 17 June 2019 (UTC)

I'm a bit afraid that the eagerness to allow anonymous authors (the founding principle many refers to) could be the main reason for failure of this project. We could, and perhaps should, allow articles and reviews to be posted anonymously, but when an article goes officially published (we need some descriptive word) it should refer to fully identified user accounts. Perhaps you upload or write a paper, then it is sanctioned until it passes peer review, but unless all users has real names it will not leave this state. The reviewers must accept the article, and the authors must accept the peer reviews. If not, an admin (the one in charge, editor?) may override and reset the accept. I wonder if an accept should convey a grading, thus both authors and reviewers could accumulate mean grades. If the accept is overridden, then the grade can't be set, but perhaps this user should be graded too. Such grading is nothing more than a specialized log. It is hard to troll such grading systems if it comes with a cost, and in our case the cost is the work going into writing the articles and the reviews.

I wonder if it would be acceptable to have non-invited reviewers that could be anonymous. Non-invited reviewers would probably only spot minor flaws, but could increase the overall quality (especially readability) of the paper. — Jeblad 11:42, 17 June 2019 (UTC)

All points noted. If anonymous authors are allowed, I become disinterested in this project — and so will researchers. Anonymous reviewers? Certainly the managers of the project need to appoint real-life reviewers and mediate between them and the authors. It's the only way to gain credibility. I very much like the idea of a talkpage after publication (presumably with responses from authors, where they wish); that doesn't affect credibility one bit. But it would need to be monitored by an admin. Copyediting still worries me a lot. The standard of expression in most journal articles is pretty bad; being strict about clarity and precision of prose (and I mean significantly stricter than you find in featured article processes on WP sites) is an way of gaining credibility. Professional-standard copyeditors are required. They do exist on WMF sites, but have to be located and rewarded by being named, I guess. Let me say: if academics could write, I wouldn't have a job. Tony (talk) 08:43, 19 June 2019 (UTC)

Thank you Tony for your substantial contributions to this discussion. You make several excellent points with which I agree wholeheartedly. I hope you will stay involved, perhaps as an expert consultant on the topics you have mentioned here. :o) Mark D Worthen PsyD (talk) 22:27, 6 August 2019 (UTC)

You're most welcome, Mark D Worthen PsyD, as are the other active editors working on this proposal. I don't often visit Meta nowadays, but do ping me at places where you want a comment. Tony (talk) 22:26, 9 August 2019 (UTC)

Some points from the Wikimedia-l mailing list thread

Some points below copied from the Wikimedia-l mailing list thread: "WikiJournals: A proposal to become a new sister project".

Quality control

There are a few mechanisms in place for quality control:

• Standard academic processes of external peer reviews which for wikijournals are all public (journals such as PLOS are moving in the same direction)
• Accountability to the academic community - indexing by cope, doaj, pubmed, scopus, web of science, free journal network etc all require extensive external auditing of processes. Each journal has to apply for these individually and they are challenging to gain and retain.
• Accountability and transparency to the wider community - unlike other academic publishing houses, we try to get feedback on ideas, votes and governance (which could be much greater with more exposure to the academic community)

T.Shafee(Evo﹠Evo)^talk 14:28, 7 June 2019 (UTC)

Why would an academic choose a WikiJournal

1. Most OA journals charge $2000-3000 per publication.
2. Idealistic academics may value it for its adherence to the ideals of the wikimedia movement (public focussed, more democratic than most journals)
3. Cynical academics may be drawn by the likely high impact that the journal will likely get form publishing a lot of broad review articles and the exposure of those through wikipedia
4. Multiple 'unique selling points' from being integrated with wikimedia to give further impact:
   • Obviously, broad review articles are also integrated into Wikipedia so vastly wider read than typical journal reviews
   • Image-based article can have their figures added to commons (e.g. doi:10.15347/wjm/2017.008)
   • It could be a way to peer review parts of wikidata (e.g. whether the Drug interactions (P769) property set is up to date, and what references should support any additions)
   • possible integration of some articles into wikiversity taught courses (e.g. this teaching case study doi:10.15347/wjm/2017.006)
5. Indirectly, I also hope it can act as a gateway drug to get more experts wanting to engage in the other projects. Because it accepts submissions straight out of wikipedia, it might also increase the incentive for an academic to contribute to wp if they can later submitting it to wj.

T.Shafee(Evo﹠Evo)^talk 14:28, 7 June 2019 (UTC)

Democracy

So far the only inherently undemocratic part of the project has been the strict requirements on the peer reviewers.

Conversely, authors have included professors, students, and people completely unaffiliated with any university. Editorial board composition ranges from the academics you'd expect to see, but also science communicators, science librarians and experienced wikimedians which are uncommon in other journals.

The indexed draft areas (currently called WikiJournal Preprints) will be a free-for-all. Currently we have no exclusion criteria other than the standard Wikimedia copyvio/slander/etc. If there become problems we might need editors to keep an eye on them like ArXiv does, but I hope to keep it light-touch.
T.Shafee(Evo﹠Evo)^talk 14:28, 7 June 2019 (UTC)

Plan S

The journals definitely intend to be Plan_S compliant. I'll raise the idea of putting out some statement of intention over at the project. Plan_S will likely have a large direct impact in Europe and the US, and likely far wider-reaching indirect ripple effects across all of academic publishing.
T.Shafee(Evo﹠Evo)^talk 14:28, 7 June 2019 (UTC)

Translation

So far there has been little translation of articles. This is possibly because the project started in English, which is especially dominant as a lingua franca in scholarly publishing. However, there have been a few proposals for translation that have been raised:

• Translation of whole articles if they are thought by the community to be particularly useful (e.g. Teladorsagia circumcincta is one of the most important agricultural parasites doi:10.15347/wjs/2019.004 yet is almost completely absent from wikimedia)
• Translation of many/all abstracts into multiple languages

From the point of view of an official 'version of record' (i.e. what the doi points to) the authors would be named along with attribution of all contributors. If there are translations, they'd likely be marked as something like "adapted by translators XYZ from article XYZ by original authors XYZ under a CC-BY license", though details would need to be decided if it came up. See this 2008 article for some ideas floated previously floated. I'll admit I've limited knowledge of translation practices though, so the project would need advice!

For some existing Wikipedia-based examples:

• PLOS article and uk.wp page
• PLOS article and es.wp page

T.Shafee(Evo﹠Evo)^talk 14:28, 7 June 2019 (UTC)

Impact and reach

I fully agree that impact factor is of primary importance to many researchers. However, many grants that fund research also have started looking for evidence that researchers are making genuine efforts in public outreach. Example: A researcher spends 30 years on one of the most important livestock parasites, publishing review articles read by 100-1000 people, yet the Wikipedia page is only 2 sentences long. Their grant reviewers, potential students, farmers, politicians, and journalists read the WP page which gives a false impression of obscurity to the topic. Then they publish a review article with a WikiJournal which is dual-published as a citable version for their cv and copied into WP to show they they are trying hard to keep the general public informed (doi:10.15347/wjs/2019.004).
T.Shafee(Evo﹠Evo)^talk 14:28, 7 June 2019 (UTC)

Citing WikiJournals in Wikipedia

I see the COI point of view. On the other hand, the best cure for coi is transparency and I think the publishing of peer reviews that go along with papers. Overall, I think WP use of WikiJournals articles as sources (e.g. doi:10.15347/wjm/2017.005) would remain independent and a matter for WP:RS discussion once the journals are accredited. However, one perennial problem in WP has notable topics lacking citable sources (e.g. first nations history / neglected tropical diseases / women historical figures). If a wikipedian were able to do the research into an aspect of that topic to a level that it meets rigorous scholarly standards and passes external peer review, then that may a be a reasonable way of minting a valuable new citable source. Again, that'd be up for the community to decide as the project progresses.
T.Shafee(Evo﹠Evo)^talk 14:28, 7 June 2019 (UTC)

Indexing

We have started the practice of drafting indexing applications publicly for greater transparency (unique as far as I know).
T.Shafee(Evo﹠Evo)^talk 14:28, 7 June 2019 (UTC)

Comparison to peer review within Wikipedia

WP essentially does post-publication editorial review (rather than peer review). External peer review by WikiJournals and internal PR/GA/FA review by wp editors perform complementary (not competing) roles. Many FA articles are definitely up to academic standards - and indeed their performance through peer review proves just that as an additional quality-assurance mechanism. That is not universally true (e.g. the review of GA article Surface tension includes "in some instances the ideas are incorrect ... It will confuse rather then enlighten readers new to the field"). FA has unique aspects that external academic peer review lacks (e.g. a sharper focus on readability, and formatting, spot-chacking of references).
T.Shafee(Evo﹠Evo)^talk 14:28, 7 June 2019 (UTC)

As an additional note on academic involvement in wikimedia projects in general, there are still >7000 articles specifically tagged as needing "attention from an expert on the subject". . T.Shafee(Evo﹠Evo)^talk 14:21, 8 June 2019 (UTC)

Wikipedia does post-publication review, not post-publication editorial review. The later would imply the review is done and coordinated by some editorial office, which Wikipedia does not have. An open and loosely coordinated group of wikipedians is not really an editorial office, even though it sometimes act as one. — Jeblad 14:53, 10 June 2019 (UTC)

Peer Review volunteering

I feel that it may be difficult to get enough people to do the Peer Reviewing. Since they have to be peers, they would generally have to be credentialed experts in their field. Peer Review is already a thankless task, and I hear that most journals have a hard time getting three reviewers for each article. Does anybody have any data on the ease or difficulty in getting peer reviewers for open source journals? Abductive (talk) 20:40, 8 June 2019 (UTC)

There are a few relevant stats on peer reviewer response rates. Currently the journals permit peer reviewers to remain anonymous upon request (~25% choose this, in line with the experiences of other journals; example). Having review comments public doesn't seem to have a reported negative effect on response rates e.g. [4] [5] [6]. There's also been quite a bit of discussion on how double-blind peer review (author identity also anonymised until publication) would affect peer reviewer response rates, with a number of references gathered on possible effects on peer review response rate and quality (discussion).

For the WikiJournals themselves, the proportion of contacted reviewers agreeing to review has massively varied depending on topic from a 75% (4 contacts, three agreed) to a <5% in one case (over 40 contacted to get 2 reviewers to agree). Since the peer reviews are already public, one option is to also publish the peer reviews as indexed, citable objects in their own right so that reviewers gain a line item for their cv (see discussion). There are therefore factors working for and against wikijournals with regard to soliciting peer reviews: 1) 'brand recognition' affiliation with Wikipedia (especially for articles intended for integration into Wikipedia) seems to be a motivator for reviewers, with many specifically mentioning this or thanking the journals for the opportunity to comment on current/potential Wikipedia articles. 2) Increasing impact factor and indexing will be important in further attracting reviewers (I've had one reviewer state that they only review for journals above a certain IF threshold!). 3) remaining flexible, dynamic, and experimental to changing peer review ideas and norms - there're a lot of ideas out there that on ways to improve aspects of peer review that can be drawn from, adapted and advanced. T.Shafee(Evo﹠Evo)^talk 04:30, 9 June 2019 (UTC)

We could make a double blind system where the user names are replaced with a user and base page specific digest, ie the digest would be the same for all contributions to a page, and where the digest is used on bot subject and talk page until they are published. It would be almost as IP6 anonymous users, but we should probably try to make something more readable. One option could be to fold into naming schemas, like “Andy Adwark”,“Benny Bull”, “Charlie Cheetah”, and so forth. By using such pseudonyms it is far more easy to discuss decently then using numbers. Compare for example to discussions at Wikipedia involving users with only IP addresses.

It could make it a lot more popular to do peer review for such articles if the reviewer was added on the page. I'm not sure if they should go in the citation, but it should be safe to put them in the footer. Including users from the talk page in the subject footer could be difficult, but perhaps we could get around that problem somehow. A simple solution could be to have a special “review” namespace, where articles are linked to the article under review, and then the main authors of this page are extracted and added to the subject footer. Usually there should only be one main author of the review page.

Reviewing an article should also be open non-invited people, but that can make it difficult to verify the scholarly background. It is perhaps most convenient to simply mark some of the reviews as “invited”. — Jeblad 16:18, 10 June 2019 (UTC)

I think you're right that reviewers probably shouldn't go in the citation, but rather in the footer or infobox. They should also definitely be listed in the wikidata item! I agree with simply marking up again, currently sort of implemented manually (example). Your idea of auto-generated pseudonyms for anon peer reviewers is interesting. It reminds me of google docs's way of assigning animal so anonymous document editors. It may alternatively be possible to name anon reviewers based on the article ("R1 (Article shortname)", "R2 (Article shortname)" etc) since it's pretty common for authors to refer to reviews are 'R1', 'R2' etc anyway. T.Shafee(Evo﹠Evo)^talk 06:54, 25 July 2019 (UTC)

Pointing to specific parts of a page

It could be nice to be able to point to specific phrases in an article, especially from a review, when the phrase is a misunderstanding or somehow convey an error. I have experimented with a simple solution where you simply make a fragment identifier, and the fragment is turned into a search pattern. It can be generalized into a LSH if the search pattern is to long. There are some UX problems that must be solved though. — Jeblad 16:28, 10 June 2019 (UTC)

That'd definitely be useful. Indeed, it could be useful in wikimedia talkpages in general (especially if eventually a citoid-style interface could be developed). Somewhat related, it'd be useful to be able to simply add simple cross-reference to a numbered figure within an article. T.Shafee(Evo﹠Evo)^talk 04:23, 11 June 2019 (UTC)

To be a bit more specific; Javascript code checks if the fragment identifier is an existing target, and if not tries to find the fragment as a search pattern inside the content. It will then mark the found match with one or more span over the whole match to highlight it, and additionally mark the containing block. I'm not sure whether the anchor should be added at the beginning of the containing block or at the beginning of the matched pattern. — Jeblad 12:47, 13 June 2019 (UTC)

Publishing points/credits vs dissemination points/credits

Not sure how this fits in, but some research institutions split publishing into what gives publishing points/credits (Norwegian: publiseringspoeng) and dissemination points/credits (Norwegian: formidlingspoeng). Some also splits publishing points/credits into several levels. At nowiki we had a discussion about getting “formidlingspoeng” for writing on Wikipedia, but as I recall it stopped on being able to measure the amount of contributions and identifying the contributors. Measuring contributions can be solved, this is nothing more than accumulated edit distance, but verifying the identity of contributors are more difficult.

In Norway the correct organization to contact is w:CRIStin. — Jeblad 17:14, 10 June 2019 (UTC)

Wikilinks

The later part of the statement “Namespace-specific default interwiki links (for articles, wikilinks should point to Wikipedia by default)”. It could be simpler to use the “w:” as prefix, but strip it as default when the link is rendered. At Wikipedia we keep the prefix as default. The reason why I say it may be easier to use the prefix but strip it as default during rendering is because we then can avoid changing the linker itself and only use the existing callback. — Jeblad 11:46, 11 June 2019 (UTC)

Interesting idea. Very useful to know that that's on option. Having said that, it'd be ideal if it were possible for the VisualEditor interface to still suggest/autocomplete wikilinks. T.Shafee(Evo﹠Evo)^talk 12:25, 11 June 2019 (UTC)

Not sure why it does not suggest autocomplete on sister projects, it should be rather trivial to implement. — Jeblad 12:16, 13 June 2019 (UTC)

Seems like phab:T188871 has gone in the deep freezer, but I believe this is a pretty important functionality for WikiJournals. — Jeblad 16:07, 15 June 2019 (UTC)

Interwiki links

comments below moved up from separate section since to keep points together T.Shafee(Evo﹠Evo)^talk 12:55, 24 July 2019 (UTC) On “Namespace-specific default interwiki links” is as far as I know difficult and would require rewriting some code. In my opinion it would also create a horrible user experience. — Jeblad 12:05, 16 June 2019 (UTC)

If possibly, I think it would be worth a try. Currently with wikijournals as implemented within wikiversity only really link to other wikiversity pages in the journal information namespages (e.g. author guidelines) and volumes/issues. The articles and preprints all link exclusively to wikipedia except for in the infobox (example). I therefore think it should make the experience of drafting an article much smoother to not have to include w: at the start of every wikilink, and hopefully the list of suggests links could be made to work. T.Shafee(Evo﹠Evo)^talk 12:39, 24 July 2019 (UTC)

Inline references

Scientific articles will need some kind of inline refs, that is a a reference pulled down on the line and written out. We don't want a ref like this but like this (Blad 2019), or some variation. One way to do this is to extract the reference mark information from the content, that is the names and year are made recognizable with data attributes or similar (microdata, rdf), and when found they are repacaged and put into the name attribute of the ref tag. The written out form of the ref tag could simply be marked as "inline", like …but like this <ref inline>{{Cite article|author=Blad, John Erling|title=On the wagging tail of a cat|year=2019}}</ref>,…. A better technical description should go on a separate page. — Jeblad 14:51, 11 June 2019 (UTC)

Many different variations are observable in journals these days, yes traditionally the (author, year) style was common place but many recent journals now number the refs with a [1] for example this article in PLOS Biology. Scott Thomson (Faendalimas) ^talk 15:03, 11 June 2019 (UTC)

This is slightly more than just the form of the reference mark itself, it is also about how we talk about a reference. In Wikipedia we very seldom discuss the reference, but in a scientific article we often discuss the results provided by some other researcher. When we do that, our present reference mark very fast gets awkward. — Jeblad 15:08, 11 June 2019 (UTC)

I get your point now sorr. To be honest I have long thought the referencing systems employed by many wikipedia ages were not the best practice, however I acknowledge it comes from a multitude of fields and not just one of academia. Most journals have reference guidlines among the author guides, further definition of referencing styles across WM may also be due. Cheers Scott Thomson (Faendalimas) ^talk 15:21, 11 June 2019 (UTC)

No problem, I'm not very good at explaining my ideas. They usually comes out in jumbled pieces! — Jeblad 15:43, 12 June 2019 (UTC)

Figure numbering

The statement “Some way of automatically numbering figures” is just one of a whole bunch of similar problems. Figures, tables, images, maps, equations, listings, etc. It seems like most of them can be solved by having a wrapper of some kind, and having VE recognize this wrapper. The code is then almost like the the Cite extension, and it could even be adjusted to create specific “reference listings” by using standardized group attributes.

A wrapper could be a tag function for the reference text itself, could even be the current ref-tag, but then it should be told to leave the text in place sometimes. In other cases it should replace the reference text with a marker. Typically for an image you would write

[[file:Example.jpg|thumb|right|<ref name="example" group="Fig" text>Some explanatory text</ref>]]

This explicit form works quite well if there is a figure caption of some kind.

The valueless attribute text tells the ref-tag to leave the text in-place. The group attribute should work as before. When collecting the references the content is reused for the list, pretty much as before.

Fig 1: Some explanatory text.

A further fix could be to show autonumbering for the text when it is left in-place, that is the current number used for markers, and add the group to the number itself. That would make it possible to get something like the example on the right side. Placement and formatting should be localized.

Because we would have to reference such markers from other places in the text we would have to name them, but also tell them to be rendered slightly different. Typically like Something about the example <ref name="example" group="Fig" inline/> with more text following… which would then render as “Something about the example (Fig. 1) with more text following…”. [Ie. the form is similar to #Inline references.] This would work for most cases, and it could even be clickable. If clickable it should be able to go to the defining place, and not just the “reference list”. This is a difficult as the defining place for a literature reference is probably the “reference list” while the defining place for an image is were it is in the article. It could be that default behaviour follow the different groups, and default should be on a double click.

A few groups should probably create ref-tags by themselves, for example equations. It should be sufficient to give the math-tag a name-attribute, and then a number would be inserted. To make the “reference list” more readable it should also be possible to inject a description

<math name="mass–energy" desc="Equation of mass–energy equivalence">E=mc^2</math>

I belive a description given as an attribute should only be used for the “reference list” and not for a caption.

This would then be referenced as something <ref name="mass–energy" inline/> and then some … and render as “something (Eq. 1) and then some …” If you want an ordinary mark it would go as something <ref name="mass–energy"/> and then some … and render as “>something ^[1] and then some …”

This is more or less according to my previous notes on this problem. — Jeblad 14:33, 15 June 2019 (UTC)

Thanks! It's very useful to know that this is possible so that we can move forward from the current manual figure formatting of v:Template:Fig! The two main features would be the numbering, and also adding the attribution under the caption (ideally author and license info populated from commons). T.Shafee(Evo﹠Evo)^talk 13:00, 24 July 2019 (UTC)

Related stuff

Yes. I am already in some trouble with numbering, both numbering of sections, and numbering within sections (of equations, theorems etc); see the last 3 paragraphs here. Tsirel (talk) 18:45, 15 June 2019 (UTC)

This is not really about section numbering, that is slightly different beast. (Still a TOC is really a kind of “reference list” but does not act like so.)

First, I believe it is wrong to put a page header into the content of the article. It creates massive confusion. The page content should be about the article and nothing more.

There should be a flag to turn of numbering of TOC, butI'm not sure this is the correct way to use the TOC at all.

Using various links that does not match creates a lot of problems, they are bound to happen. Even a plain link into a page may create havoc. — Jeblad 20:28, 15 June 2019 (UTC)

Import and export

There are two statements; “Simple on-wiki forms for users with no wikimarkup experience” and “Ideally we would like converters to wiki from DOCX and LaTeX so that articles can be more easily submitted.” that are really about the same thing. We need some mechanism to upload (and also download) articles in various formatting, or at least do it as best possible. I believe this can be solved quite easily as a special page using pandoc. This document converter can handle an amazing number of formats. During import we would convert from an implicit format given by the suffix, or from an explicit chosen format from a drop down list, and then convert that into Mediawikis format. During export we will chose a format and then download that. We probably can't build complete articles with all images and files, but we can upload and download parts that make reassembling the articles possible.

Note that pandoc is a bunch of scripts, and inherently unsafe. The security problem it poses is similar to ImageMagick, which we also use, but it possibly even higher in this case. It could be interesting to open a discussion on whether it is possible to use this tool or not.

There are already special pages for importing and exporting articles using the Mediawiki xml-format, I'm not sure if this should be an extension of those pages or be something new. I wonder if the existing import and export is really load and save of existing articles, and not about import and export to alien formats. — Jeblad 11:54, 16 June 2019 (UTC)

Sidebar items

On the statement “Specific left menu items”, this is done on the project by editing Mediawiki:Sidebar. Remember to create the additional system messages so they can be localized into additional languages. — Jeblad 11:55, 16 June 2019 (UTC)

Yes, hopefully this would be relatively simple tom implement, but would make a big difference to usability if a separated site. T.Shafee(Evo﹠Evo)^talk 10:53, 28 June 2019 (UTC)

Namespace-specific formatting

Namespace-specific formatting is done in Mediawiki:Common.css, there is a set of classes ns-* for adapting the format. If this is really about header and footer then there are several extensions that changes the appearance of the page, but usually they should not be used. The only case I can imagine where this is useful is when a namespace is somehow published separately, but in those cases the header really belong to the separate publishing and not in the namespace. — Jeblad 12:04, 16 June 2019 (UTC)

It's partly about making sure that draft:/preprint: namespace is clearly visually different without having to rely solely on a template if possible. For example, every article page should have an v:Template:Article info automatically, ideally with all parameters auto-populated from wikidata. Volumes and issues would need a different header and possibly a separate namespace could be sensible depending on how it operates. They can be added by making sure to copy correct templates across but it'd be nice. Similarly, pages in another namespace currently use v:Template:WikiJournal_h2 to manually format level two headers. T.Shafee(Evo﹠Evo)^talk 12:16, 24 July 2019 (UTC)

Transclusion/import/export

There is a system for scary transclusion in Mediawiki, but I'm not sure it will work properly for this kind of articles. Main reason is we would import the article as-is, but on Wikipedia the article needs an into at beginners level, before it dives into the more difficult parts. This beginners intro often partly replaces the introduction in a paper. If we had an optional beginners intro then it might work, but I'm still not sure whether the rest of the content would follow the assumed style conventions.

Ordinary import/export should be possible, but expect a fair amount of post-editing. To much of special formatting could create problems. — Jeblad 12:20, 17 June 2019 (UTC)

Plain import/export could be viable if two issues are solved: 1) interwiki links to wikipedia as default in article namespace and 2) different default figure formatting using the same syntax. Currently all wikilinks have to be manually converted using v:Template:Convert_links and figures manually formatted with v:Template:Fig. (importing from wikipedia and exporting back to wikipedia current guidelines) T.Shafee(Evo﹠Evo)^talk 12:51, 24 July 2019 (UTC)

Note taking feature (wishlist)

There should be some way to make private notes about an article. This is partly about collecting articles and partly about taking notes for those articles. This probably belong on a future wishlist and not on a first requirement list. — Jeblad 10:39, 24 June 2019 (UTC)

Agree. I suspect that it could be a feature that readers of other wikimedia wikis might like as well to privately annotate articles as they read and share those annotations if they choose. There are several commercial ones at the moment (e.g. I think https://web.hypothes.is/ may be open source). I don't know if any of the existing platforms are compatible, otherwise that sort of thing could be within-remit to develop. T.Shafee(Evo﹠Evo)^talk 12:20, 24 July 2019 (UTC)

Universities as sponsors?

I wonder if it could be an idea to have some well-known universities as sponsors. Such sponsors could have a special responsibility to vet articles, that is make a first coarse review. At some point the community would be big enough to do this themselves, but initially that could be pretty hard. Just figuring out if something is an accepted field of scholarly research could be pretty difficult and at least time consuming. Having some sponsoring universities that knows the various fields could save a lot of time.

Which brings me over to another of my pet-projects; we need a mechanism to notify subscriptors about specific topics, perhaps by “tagging” articles. In this case we could use the tags used on typical articles, like “Computer Science - Machine Learning”. If you subscribe to a tag, then you will get a notification when a page gets tagged.

Someone doing peer review would be asked to review a paper, but university sponsoring a field would have people subscribing to one or more tags. Of course ordinary users should also be able to subscribe to tags.

Sponsoring universities could have specific user boxes, but that could be abused. Somehow the user boxes must only show a valid state if the university endorses the user. Perhaps a guild-model is better, where a user (the official university account) endorses its associated users, and the user box shows this state. Users could also endorse each other. The later was my initial take on this idea, I would like to use endorsement to promote users to administrators. In this case endorsement to a university guild could be the sole responsibility of a university, or endorsement to reviewer could be done by the community or a subpart of the community. — Jeblad 21:12, 2 July 2019 (UTC)

I really like that idea. Universities would give our content a sense of authority and, hopefully, reliability. Universities would also attract students of those universities to become involved in the project. SelfieCity (talk) 22:45, 19 July 2019 (UTC)

Fully agree with this. Approaching universities for endorsements will likely have to grow in parallel as the reputation grows. The same thing goes possibly even more for scholarly societies (like how Wikiproject computational Biology has a partnership with the International Society for Computational Biology). There are whole academic societies devoted to fields that have a single wikipedia page on the entire topic (example). Any endorsement of individual users would probabnly be best done via their employer status in wikidata using a faculty webpage as the reference. Currently if someone claims affiliation with an institution we, again, check that manually.

I also agree that notifications and emails would be great to improve. Currently we have to manually send out emails on course-grained mailing lists when new articles are published! T.Shafee(Evo﹠Evo)^talk 12:30, 24 July 2019 (UTC)

Great idea Jeblad! :0) Mark D Worthen PsyD (talk) 22:35, 6 August 2019 (UTC)

Point DOIs to a certain article version

I think we can use this extension https://www.mediawiki.org/wiki/Extension:Approved_Revs

This will point to the most recent, peer-reviewed version of the article.

Two ideas for the future:

1. Maybe consider having an anonymous peer-review of 3 authors for the first submission, and then for each update request, a public peer review?
2. Have the public peer review being continuous, and while only the author could edit the article¹, the public can rate the edits with https://www.mediawiki.org/wiki/Extension:FlaggedRevs ?

These ideas are for after WikiJournal is accepted by WMF and widely recognized. It's good to be conservative and seek establishment first, and not try to innovate too much.

¹To restrict editing to the original author, those extensions could be usefull:

• Lockdown/AuthorProtect – only author can edit
• ArticleProtection - for only original creator
• UserPageEditProtection - only user can edit their own USER page

MavropaliasG (talk) 07:14, 17 August 2019 (UTC)

en.wp Watchlist-message

As an additional route for informing the English Wikipedia community, I've suggested a Watchlist-message (wording discussion). There's a list of plocactions that have ben informed at this page. Any further suggestions or dissemination welcomed. T.Shafee(Evo﹠Evo)^talk 02:02, 21 August 2019 (UTC)

Is it sustainable?

The submission reports that almost all peer reviewers only review once.

This seems to suggest that you are (or would be) relying on only a few very active souls, and the loss of a few could render the project with enormous backlogs? (please ping) Nosebagbear (talk) 08:14, 21 August 2019 (UTC)

@Nosebagbear: Indeed a very good question: relevant to both sustainability and scalability. Organising external peer review is likely to remain the rate-limiting step, so (current guidelines). For WikiJSci/WikiJMed/WikiJHum, there are a few key items:

1. Associate editor recruitment will be key. These are the users who will be going out to contact external reviewers on an article-by-article basis.
2. Growing a spontaneous reviewer and copyeditor community who may not be specialists, but can comment on readability, style, diagrams etc.
3. Technological solutions to automate many of the time-consuming tasks (technical wishlist).
4. Partnerships with outside journals, academic societies and institutions to assist in contacting peer reviewers (possibly even WiR format).

I think making sure the journals each have critical mass to be self-sustaining is very important. It's part of the reason why WikiJSci and WikiJHum have such broad scopes, since we recked that narrow-scope journals were more at risk of falling under that critical mass of editors (at least initially). T.Shafee(Evo﹠Evo)^talk 12:55, 21 August 2019 (UTC)

Some basic questions

I have just become aware of the WikiJournal project, through a banner notification on Wikipedia of a proposal being discussed on meta. I looked at some of the existing journals here (particularly WikiJournal of Medicine), but still could not find explicit answers to some basic questions:

1. Format of the submission. Does an article need to be submitted as an editable Wiki page? If not, what other alternative submission formats are accepted? Pdf? MS-Word? LaTeX? Postscript? DVI? Something else?

2. What exactly happens with articles that were submitted to a journal as WikiJournal Preprints but is eventually declined by the journal? Does the record of the fact that they had been submitted and declined remain at the preprint's page? What about peer and external reviews?

3. What happens with conflict of interest statements that involve specific personality conflicts? E.g. if the author requests that certain specific researchers NOT be used as referees for some reason? Is this information included in the article when the article is published in a journal?

4. Similar to Q1: In what formats can external reviewers submit their reviews? E.g. can they submit a PDF file? A plan text file? Or just as an editable wiki page?

Thanks, Nsk92 (talk) 09:14, 21 August 2019 (UTC)

I saw these comments first over at this page, so have put a comment there. T.Shafee(Evo﹠Evo)^talk 12:40, 21 August 2019 (UTC)

I am replying to your last post at WikiVersity here since over there my edits keep being blocked by the overly aggressive automatic edit filter. For your first question, no, not yet. I would want to see such a converter operational first, see how well it works, how easy it is to use it, etc. Even with a converter, hypothetically, becoming available, the punch question will be whose responsibility it would be to do the conversion. If the submitter is required to perform the conversion and the fine-tune it, I expect that would severely limit the pool of interested authors, simply because almost all of them have no familiarity with MediaWiki at all and won't be willing to take a risk performing an unfamiliar procedure on the fly, while submitting an article. If the editors would be responsible for converting a paper submitted in latex, that may be appealing to more authors, but one would have to see how much extra burden and work that would put on the editors. The best thing would be is if the editor submits a latex file, the converter automatically creates a MediaWiki file and then the submitter only has to preview it and push the "approve" button or something like that. That's essentially how arXiv works when you submit a latex file. However, at the moment all these options are too hypothetical. I don't know if they are technologically feasible, what the various technical obstacles are, etc. Most LaTeX files now load a variety of LaTeX packages, have user defined macros, etc. It is a really complicated thing. I have no idea if a reasonable automatic converter handling all this stuff is even possible. Nsk92 (talk) 13:22, 22 August 2019 (UTC)

About your other point, regarding preprints serving as a form of scoop protection and making an earlier priority claims/stake. Yes, in disciplines like math and physics this practice has become standard during the last 10-15 years. In math most papers now are posted to arXiv first as preprints (although there is significant variation between different areas of math in this regard), and then it could take several more years before the paper is officially published in a journal. However, life sciences are completely different. Over there, unlike math, refereeing and then publishing a paper in a journal takes a few weeks, maybe months, but not years. For that reason priority is assigned strictly by publication date. In medicine in particular, people doing modern cutting edge would not entertain the possibility of releasing their paper first in a preprint form and then waiting for an undetermined period of time for the paper to be reviewed, revised and maybe declined by a journal. It may be that some years from now their practices will change, but that's how things are at the moment. In order to have any chance of attracting high level contributions in life sciences now, authors must be given the option of submitting a paper in a non-public form, where it would only be visible to the authors, editors and reviewers. I don't think that the WikiJournals model can accommodate such an arrangement except (except on an ad hoc basis, as exceptions for a small number of papers). In order to do this systematically, a parallel article handling system would have to be set up for handling non-public submissions. The files would have to be hosted on a different site, not as MediaWiki preprint, with specific password/authentication requirements for accessing the files. Nsk92 (talk) 13:40, 22 August 2019 (UTC)

By the way, I would also be interested to know if any of the three existing WikiJournals have ever declined an article? Or has the acceptance rate been 100% so far? Nsk92 (talk) 13:47, 22 August 2019 (UTC)

Let me also articulate in more detail some of the other issues related to the proposed model and the use of MediaWiki. Even if it becomes possible to submit a paper as a latex file, and then have the converter post it as a preprint in MediaWiki format, the issue of revisions will face a similar problem. You would have to be prepared to take a revised version again in LaTex format, then convert it to MediaWiki and post as a complete replacement of the previous MediaWiki preprint. The substantive revision work by the authors would still need to be conducted off-site, privately, by the authors in their internal discussions. Revising a modern scientific paper is a complicated, labor-intensive and private endeavor. It usually requires either e-mailing the paper back and forth between authors, with various comments between them, or having the paper stored in a group folder on some file sharing site like Dropbox, where various marginpar comments are made and responded to by the co-authors, the paper slowly changes, often quite significantly, etc. The process can take months or even years. Nobody in their right mind would want to make this internal revision, discussion and deliberation process public and expose it to the world. The only exceptions might be true Wikipedia enthusiasts and occasional solo authors of survey papers. Everybody else will want to keep the process of developing and revising the paper non-public. It is too sensitive and unsuitable for being shared with the world, and not just because of the priority considerations. By the way, a glaring gaping hole in all three of existing WikiJournals is that they don't provide explicit up-front large bold font author information and instructions about the format in which the papers are accepted (MediaWiki) and about how and where the authors can prepare such a paper before submitting it. The lack of such information is an unacceptable weakness, even for a limited pilot project as it exists today. You cannot simply say that the authors should use the submission form and have them figure out from the submission form what's what. You absolutely must provide detailed, explicit and easily visible and accessible information about the format in which the papers can be submitted AND about where and how the authors can prepare papers in that format before submitting them. Nsk92 (talk) 14:14, 22 August 2019 (UTC)

Regarding declined articles: OR example, review example (category). However so far the WikiJournals have tended towards leading authors towards overhauling articles if possible and sending them out to the peer reviewers again, so overall acceptance rate has been high (though hopefully transparency of the reviews makes it easy for readers to check the stringency of the peer review on an article-by-article basis). Note that most journals have a higher acceptance rate for review articles than OR, so this may be somewhat skewed by that. Regarding versioning, if an importer was functional, I think the crossmark versions in combination with the diffs should be clear. See also the comments section #Further_research_on_top_of_paper_published_in_WikiJournal below for similar notes. You make a good point that the information should be updated in the "submissions" tab for each thought (transcluded from v:WikiJournal_Preprints). I'll try to better cover those aspects whilst trying to be concise to avoid guideline-overload. You're welcome to suggest wording if you've opinions on the specifics. The non-wikipedians that have used it so far have managed relatively well with VE, with the main problem being reference misformatting. Eventually, I would like to also have short video walkthroughs (but that's obviously an optional extra). T.Shafee(Evo﹠Evo)^talk 14:39, 24 August 2019 (UTC)

What is the intended format of articles? (feature vs. review vs. textbook vs. extended wp page etc.)

(Came from central notice at en-wp.)

In the science journal, there are two articles whose topic I have some familiarity with: Lead, Binary search. Neither is really what one would find in a scientific journal; they look more like a textbook on the subject than a review article (too much focus of what "everyone knows" and too little focus on the state of recent literature), and do not contain any original research that I can see. Giving a very quick look at other articles gives me the impression it has the same format - basically, it's a longer Wikipedia article that underwent peer review.

Reading the proposal page, one would expect (on the contrary) publication of feature articles (i.e. original research) with maybe a few review papers in-between. Which is it? Is the focus supposed to change with a move towards original research articles (in the usual format introduction-methods-results-analysis-conclusion)?

(Either would be a fine project, but some clarity would help.) Tigraan (talk) 12:30, 22 August 2019 (UTC)

I suspect that the WikiJournals will always have a strong focus on review-style articles (more similar to Nature Reviews X or Advances in X journals in that regard. At the moment the focus has been the sorts of broad review articles that can be reformatted as Wikipedia articles. How common these are in journals varies a bit from field to field (though the lead article is particularly broad) - very broad review articles are relatively common in biology fields (indeed this project was partly inspired by PLOS Topic Pages). There's also been a general erosion of the boundary between a book chapter and a journal article (example book chapter that's basically as review paper that's pretty close to w:cyclotide). I'm also hopeful that more narrow articles may become more common that only relate to a single section of a Wikipedia page (e.g. Wikipedia's Hepatitis D page currently has no epidemiology section). Any review article where the authors would intend material to be also copied to wikipedia needs any OR to be kept to defined sections that can be omitted from wp (current guidelines). However, having said that, OR articles are entirely possible and submission of such articles may become more common as the journals' profiles grow. There's been talk of splitting review-only and OR-only journals, but it is likely more sensible to merely collect articles by their format in different categories. However this might change if newer journals start upon a Wikimedia Journal hosting platform. Several society journals are struggling with running costs at the moment and a flexible platinum OA platform could be highly attractive. T.Shafee(Evo﹠Evo)^talk 13:53, 24 August 2019 (UTC)

en-WP Village Pump

Please note that I have opened a discussion about an aspect of this at en:Wikipedia:Village pump (policy)#WP:JAN / WikiJournals. - Sitush (talk) 11:00, 23 August 2019 (UTC)

Reorganize "Discussion" section?

The "Discussion" section is getting larger at any moment. Shall the votes be split into support/oppose/neutral/General discussion? George Ho (talk) 20:10, 23 August 2019 (UTC)

Since I'm clearly an interested party in the discussion, I think others should decide whether a reorganisation aids readability. T.Shafee(Evo﹠Evo)^talk 13:17, 24 August 2019 (UTC)

I think User:George Ho suggestion is perfectly reasonable and anyone should be free to do so. Doc James (talk · contribs · email) 18:34, 24 August 2019 (UTC)

Ok, in that case I've done the reorganisation tp Support / Comment+Neutral / Oppose. Could someone do a quick check that the neutral/comment section is logical? Please move any comments if their current location is misleading. T.Shafee(Evo﹠Evo)^talk 10:02, 25 August 2019 (UTC)

Further research on top of paper published in WikiJournal

When a paper is building on top of previous research or replicating a previous study (i.e. something done in the past), authors usually reference it. What about something done in the future with relation to publication date? MediaWiki format would allow to add stuff to the paper page after publication. For example, if someone publishes a replication study for something that was published in the WikiJournal. Are there any plans to have some kind of post-publication section on pages of published papers? —⁠andrybak (talk) 08:51, 24 August 2019 (UTC)

Absolutely, Indeed mediawiki's transparent history makes it particularly adapted to this. There a re a few possible facets:

1. Post-publication review comments on the talkpage. There have been attempts in other journals to dome something like this. Sadly PubMed Commons closed down citing low usage, however a number of other journals do so.
2. Correcting errors in articles with clear and transparent versioning.
3. Adding new information to articles or adding additional update sections to the bottom of articles - both with clear and transparent versioning. e.g. living reviews, new examples, better figures, or even textbook-style versioning (addressing this phenomenon: 2002, 2006, 2009, 2012, 2013, 2017...).

Points 2 and 3 would require minting a new DOI via crossmark after any meaning-changing edit after checking by a reviewer so that any citation is pointing to the specific version in question. T.Shafee(Evo﹠Evo)^talk 13:34, 24 August 2019 (UTC)