Add JOSS to pubmed

[pjotrp]

Pubmed is a resource for biomedical publications. Getting a paper listed is critical for career development in bioinformatics.

We have to find out what it takes to get a publication listed (volume and issue identifiers will help) on pubmed. Maybe we can submit papers individually or have them harvested on some tag/identifier as in https://github.com/openjournals/joss/issues/124. I'll try to submit GeneNetwork once we have those.

[arfon]

On PubMed:

Has there been any new developments on this front, and is there anything an eager bystander can help with?

Some. @tarleb and I are working on some updates to the document production toolchain for JOSS to product JATS output. Hopefully this should be complete in the next couple of months and this should allow us to provide these files to PubMed for indexing.

On Scopus:

By the way, I had a look in my mailbox and the mail latency for questions to titlesuggestion@scopus.com was quite good (1 day). Thus, it might be worth getting in touch with them how to proceed. More concretely one could ask if there is the possibility of writing a "rebuttal" letter when reproposing the journal for inclusion in scopus.

This sounds like a good idea. I will try to find some time to work on this as it's an important topic for our authors but I confess a combination of lack of time and lack of affection for Scopus are dual challenges for me here...

[MikaelSellin]

Sounds great with the progress on the PubMed indexing front, @arfon. For us in the biomedical research community, this is really the one portal everyone uses to discover new science (and hopefully soon new science software). It has been a pleasure for us interacting with JOSS. But, I also notice that among fellow biomedical researchers, JOSS remains largely unknown, which seems like a shame considering the central role software development now has in our field. PubMed-indexing would go a long way towards amending this lack of visibility. Don´t take this as a stressor, simply some optimistic cheering on from the sideline. Thanks for all the hard and altruistic work by you and all the JOSS affiliates.

[tknopp]

I am also cheering from the sideline but its really like Mikael said. In order to get more attraction it is crucial to get into the indexing services. I love the idea and the excellent work behind JOSS but right now I would probably use another Journal in many cases since the downsides are too large at the moment. Although I really dislike the current system, as a matter of fact, citations are the currency in academic world (at least in Germany).

@arfon: I could offer getting in contact with Scopus and ask if it is possible to send a rebuttal letter if you want. Would put you in CC.

[kephale]

Some. @tarleb and I are working on some updates to the document production toolchain for JOSS to product JATS output. Hopefully this should be complete in the next couple of months and this should allow us to provide these files to PubMed for indexing.

Just checking to see how this has been going. We've been preparing a submission for JOSS (https://arxiv.org/pdf/2110.00601.pdf), but PubMed indexing would be really useful for NIH purposes.

A related question, will these updates mean that existing JOSS papers can be indexed by PubMed? e.g. could we submit anyway and assume that this will eventually be resolved in the future?

[tknopp]

I can only speak for Scopus and they do not index existing papers prior to acceptance into the index.

[tarleb]

Development of the JATS toolchain had to go on a hiatus for a few months, but now we are back at it. We currently have JATS files for 1332 of the 1443 published papers. The last 10% all require at least some manual fixes to the input files, e.g. to allow the proper conversion of math formulas. There is no detailed timeline, but we are making good progress.

[tarleb]

There is now PR #1022, which adds a JATS XML archive. The files all pass the JATS DTD validation at https://validator.jats4r.org.

[janfreyberg]

Does the completion of this mean Pubmed will start indexing JOSS?

Checking on the journal in the NLM catalogue indicates no, so far: https://www.ncbi.nlm.nih.gov/nlmcatalog/101708638

Will this be possible now?

[arfon]

Will this be possible now?

Yes, it should be, although I've not managed to investigate how to get indexed thus far. Do you happen to know @janfreyberg?

[tknopp]

https://www.ncbi.nlm.nih.gov/pmc/pub/addjournal/

[janfreyberg]

So it looks like the initial application is relatively small, with more effort required during later steps (scientific quality review, and technical review).

The application is supposed to be handled by the publisher. Is there an editor on the JOSS team with remit for biomedical work who has the bandwidth to submit the applications? I'd be keen to help support this but am not an editor. Looking at the editorial board, maybe @Kevin-Mattheus-Moerman would be the right person?

[janfreyberg]

Hello, I just wanted to check if anyone knew who could drive this forward?

I also wanted to tag in some people who might be interested in the same - @emdupre, @mikldk @oliviaguest @chartgerink @prashjha all seem like editors who might be interested in seeing papers PubMed indexed.

Again, very happy to contribute and support this application as much as possible.

[mikldk]

I would be willing to help on this, yes.

[chartgerink]

I'd also be happy to support this effort in my role as an editor - I figure we should form a working group to go through all the steps in the application prior to applying, given that there is only one application every 24 months.

[janfreyberg]

Thanks both, that's amazing news!

Great suggestion @chartgerink - we can either collect the responses in this issue or start a new one?

For the initial application, I've just opened up the web form. Here are the questions & answers as far as I have them:

Page 1:

• Title
  • Journal of Open Source Software
• Sponsoring organization name
  • NumFOCUS
• Sponsoring organization URL
  • http://numfocus.org
• Country/Territory
  • United States
• Publication start year
  • 2016
• Publication frequency
  • Other
• Estimated number of peer-reviewed articles per year
  • 250
• In what format is the journal published?
• ISSN (electronic)
  • 2475-9066
• Is the entire journal open access?
  • Yes
• Are all articles published fully in English?
  • Yes
• Journal website URL
  • https://joss.theoj.org/
• Aims and scope (URL)
  • https://joss.theoj.org/about#submitting
• Names and Affiliations of the Editorial Board (URL)
  • https://joss.theoj.org/about#editorial_board
• Editorial policies (URL)
  • https://joss.readthedocs.io/en/latest/editing.html#expectations-on-joss-editors
• Peer Review Process (URL)
  • https://joss.readthedocs.io/en/latest/submitting.html#the-review-process
• Policies on Conflict of Interest, Human and Animal rights, and Informed Consent (URL)
  • https://joss.readthedocs.io/en/latest/reviewer_guidelines.html#joss-conflict-of-interest-policy
  • AFAIK, there is no policy on Human/Animal rights or Informed Consent. I think this should be added given that some biomedical software packages do provide data for examples.
  • (NB: this isn't a required field in the application)
• Data sharing policy (URL)
  • As above, currently there is none, but one should (IMO) be added
  • (NB: this isn't a required field in the application)

Page 2

• Publisher Name
  • Open Journals
• Organization Address
  • ?? (@arfon)
• Publisher website (URL)
  • http://www.theoj.org
• Business Structure
  • Non-profit organization
• Names and titles of organization owner and executives
  • ?? (@arfon)
• Parent or related companies, and/or subsidiary organizations associated with the organization (include the names, URLs and relationship to applicant)
  • None ??
• Enter 'none' if your publishing company has no parent companies, related companies, and/or subsidiaries
• How do you select editors for your journal(s)?
  • ??
• Management team members
  • I assume this would be the steering council? https://github.com/openjournals/governance/blob/master/people.md
• Provide a summary for each member of the publisher's senior management team (e.g., executive editor, publishing director, managing editor, ethics manager, etc.).
  • NB: I can open issues for each individual management team member, but some may prefer to disclose these privately?
  • Name and title:
  • Responsibilities:
  • summary of responsibilities
  • Prior experience in scientific publishing:
  • Membership in professional associations:
• Publisher Policies
  • These are all required in the web form. We could just link to the JOSS ones here, with a as well as a link to the governance document for Open Journals which states that policies are delegated to journals?
  • Editorial policies (URL)
  • https://github.com/openjournals/governance/blob/master/governance.md#editorial-policies-and-processes
  • Peer review policy (URL)
  • N/A
  • Peer review policy (URL)
  • N/A
  • Advertising policy (URL)
  • N/A
  • Research ethics policy (URL)
  • N/A
  • Informed consent policy (URL)
  • N/A
  • The process for handling cases requiring corrections, retractions, and editorial expressions of concern (URL)
  • N/A

[Kevin-Mattheus-Moerman]

I have very little bandwidth at the moment to help (perhaps things improve over summer) but would be happy to help answer questions and be a relay point between yourself and the rest of the AEiC team.

[chartgerink]

Thanks a bunch @janfreyberg!

I created a Google Doc for us to start working through steps 1-6 (the application is only step 1).

We can probably uncover some hurdles in later steps that need to be resolved before applying.

[vnmabus]

We submitted to Web of Science a few weeks ago but haven't heard anything back yet.

Any update on this?

[chrisamiller]

I added a few responses to comments in the Google Doc linked above that may help. Though I'm not on the editorial board or anything, happy to do what I can to help push PubMed acceptance along

[chartgerink]

I apologize for not picking this up sooner - I am a bit overcommitted and have not been too structured about my JOSS time. I have now blocked 1h each week to work on JOSS related activities and will use that to also work on this! 😊

[paloha]

Hello @arfon & @tknopp, are there any news on the Scopus rebuttal? I am very pleased to have discovered this journal. For almost 2 years, I am observing the updates here in this issue because I would be excited to publish one of my packages in JOSS. But the fact it is not indexed in Scopus or Web of Science discourages some coauthors from doing so. Thanks for the update. Cheers

[chartgerink]

Hi @paloha - fwiw I am the one pushing PMC indexing along and we're waiting on finalizing one or two things in the JATS/XML before we can submit our application. I hope to be able to do that this year still.

[paloha]

@chartgerink thanks for quick reply. Do I understand it right, that finalizing JATS/XML will lead to submission of an application to PMC? Does this also somehow relate to indexing in Scopus and/or WoS?

[chartgerink]

Yes it is the final step for our submission application to PMC! 🥳

I am not 100% about the relation to Scopus/WoS - I responded as this thread is about PMC. I figure it doesn't hurt 😉 If you're specifically interested about Scopus/WoS only it might be good to start a new thread.

[arfon]

I am the one pushing PMC indexing along and we're waiting on finalizing one or two things in the JATS/XML before we can submit our application. I hope to be able to do that this year still.

@chartgerink – can you remind me what we're waiting at this point? I know that @tarleb has (I think) addressed all of the issues with the JATS XML at this point.

Hello @arfon & @tknopp, are there any news on the Scopus rebuttal?

@paloha – we're actually eligible to apply to Scopus again now (since more than 2 years has passed). I will endeavour to do this before the end of the year.

[paloha]

Hello @arfon, thanks for the update. Shall I still create a new issue as @chartgerink suggested? Being indexed in Scopus & WoS is a game changer because some institutions measure the performance of their researchers by the metrics of Scopus or WoS. So unfortunately, sometime a paper published does not "count" if not indexed in those.

[chartgerink]

@arfon - I've been out for a few weeks so it might've been fixed. The main issue that I remember was that we needed to change something about the images (last I checked it had relative path names only). I believe we needed to submit the images alongside the JATS/XML - I am getting back up to speed now after my vacation. Will try to figure this out this week.

[pydemull]

Hi all, I was wondering if there has been some news since the last message from this issue. I have recently published a paper in JOSS and I expected it would be added to my PubMed records list but when I see this discussion it seems that it is not yet something that is possible for "normal" JOSS papers (ie, without a particular funding as those from NIH for example). @samhforbes do you have any idea about what is currently possible to do to have a record on PubMed ? (maybe nothing for this moment ?).

[arfon]

@chartgerink @tarleb – I think we should have the images issue fixed now. @tarleb – can you confirm?

[samhforbes]

Hi @pydemull it doesn't look like this is currently possible I'm afraid, although someone else might be able to correct me.

[tarleb]

@arfon: To the best of my knowledge, all image issues have been fixed.

The JATS file for each paper is in joss.xxxxx/10.21105.joss.xxxxx.jats (not .xml); images are placed in a media folder next to the JATS file. The image paths used in JATS files are relative the file, e.g., media/results.png.

[arfon]

⚡ thanks for confirming here @tarleb. @chartgerink – I think this addresses the issues we had here correct?

[chartgerink]

Yes indeed! 🚀 Thanks for the push on this issue @everyone 😊

I am moving forward with the submission to PMC! Will post here when I'm done filling out the forms (doing it today).

[chartgerink]

Of course an error happens now:

Emailing...

[chartgerink]

PMC hid a few questions in the form, pending a few final pieces of input I can submit this. I'll post here when I've done that. 🙌

[drcandacemakedamoore]

Any progress on this issue @chartgerink ? Is there anything we can do to help from the outside (I'm a potential submitter of more papers who hopes this will be Pubmed indexed ASAP)?

[chartgerink]

Thanks @drcandacemakedamoore! We're waiting on one email thread being resolved and then the application will go out!

I will post here when that's done. Sorry it's taking so long! Never expected it to take this long.

[vnmabus]

Any update on the Web of Science status? The Google Doc is no longer available.

[arfon]

Any update on the Web of Science status? The Google Doc is no longer available.

It's over two years since we submitted to WoS and as far as I know, we never heard back. We're planning a resubmission this spring.

[chartgerink]

This issue is about PubMed Central - please use another thread for Web of Science.

PMC is still ongoing. Google doc is no longer active because we moved on from that. Submission is imminent.

[chartgerink]

I just sent the application to PMC! 🥳

✅ Step 1 of 6

[iskandr]

Did they get back to you at all?

[chartgerink]

@iskandr I will post here as we progress throughout. I have no information as of this point.

[arfon]

It's over two years since we submitted to WoS and as far as I know, we never heard back. We're planning a resubmission this spring.

Just a brief update to say that we've just resubmitted JOSS to Web of Science.

[chartgerink]

Also a short update from PMC: We received additional questions that we need to clarify in the JOSS policies, which we're working on. Here's a thread of issues we need to resolve to continue the process, as these require updates to JOSS directly.

Open all the details

- [x] First, we noted that the journal has a clearly defined conflict of interest policy for reviewers and editors, however, we were unable to locate any information about the journal's policy on conflicts of interest as it relates to authors. Please provide a link to the description of this journal policy. - Please find that through the following link - https://joss.readthedocs.io/en/latest/submitting.html#conflict-of-interest-policy-for-authors - [x] Next, can you please clarify the journal’s policies on corrections and retractions? Specifically, does the journal publish separate notices of correction and/or retraction with their own unique citation information? When reviewing an application, NLM looks for conformance with guidelines and best practices for the handling of corrections, retractions, and expressions of concern (e.g. ICMJE's [Recommendations for the Conduct, Reporting, Editing, and Publication of Scholarly Work in Medical Journals](http://www.icmje.org/icmje-recommendations.pdf), and COPE’s [Guidelines for retracting articles](https://publicationethics.org/files/retraction-guidelines.pdf)). - We post a notice at the end of the review thread ([example](https://github.com/openjournals/joss-reviews/issues/1277#issuecomment-667670005)). We also update the paper to make it clear that it has been retracted, and link to the retraction notice ([example](https://joss.theoj.org/papers/c44313ada36f12eebbaff10eb0888071)) - [x] As described in more detail in PMC’s policies on[ corrections](https://www.ncbi.nlm.nih.gov/pmc/about/guidelines/#corr) and[ retractions](https://www.ncbi.nlm.nih.gov/pmc/about/guidelines/#retr), PMC requires the submission of separate notices of correction or retraction, which must be labeled and published in citable form; that is, the correction or retraction should be readily discernable in the table of contents (or archive) and must be associated with identifiable e-location information (e.g. article ID). Once deposited, PMC creates links between corrected and retracted articles to their corresponding correction or retraction notice ([example](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3339402/)). These practices are in line with the best practices linked in my previous email. JOSS’ current method of adding a comment to the original peer review history thread in Github would not meet PMC’s requirements. Would JOSS consider updating its correction and retraction practices going forward to be in line with best practices? - [x] Lastly, we were unable to locate a table of contents or some other option to view journal content by publication year. During the scientific quality review for PMC, the reviewers generally look at published articles from the last two years of content. The ability to locate and access older articles or articles from a particular time period, whether through a Table of Contents/archive or through date/volume/issue filters, is consistent with the recommendations of[ PIE-J: The Presentation & Identification of E-Journals](https://www.niso.org/publications/rp-16-2013-pie-j) (NISO RP-16-2013, see section 2.6 Access to Content). Please let us know if earlier journal content can be accessed some other way besides clicking to the ‘Next’ page in the list of article at https://joss.theoj.org/papers/published. - We allow for filtering of year as follows https://joss.theoj.org/papers/year/2016 https://joss.theoj.org/papers/year/2017 ...etc - [x] Thank you for providing the direct URLs, however, is there any way for users/readers to navigate to these pages from the journal website, or are these pages only accessible if a user knows the direct URL? Additionally, I noticed that the pages where content is filtered by year appear to display all papers (i.e. also includes pending/non-peer-reviewed papers). When I click the filter for ‘Published papers’ however, it goes back to displaying all papers regardless of year. Is there any sort of table of contents for published/accepted content to facilitate browsing by publication date, volume, or issue? > We have now a Table of Contents page where papers can be browsed by year/volume/issue: https://joss.theoj.org/toc It is linked from every page in the footer. - [x] How long can something stay in [pending](https://joss.theoj.org/papers/active)? Do articles ever get the boot from the pending stage? - [x] Does the journal have any update policy? Since code bases and technology update overtime, is there an expectation for the articles to be living documents?

[arfon]

As described in more detail in PMC’s policies on corrections and retractions, PMC requires the submission of separate notices of correction or retraction, which must be labeled and published in citable form; that is, the correction or retraction should be readily discernable in the table of contents (or archive) and must be associated with identifiable e-location information (e.g. article ID). Once deposited, PMC creates links between corrected and retracted articles to their corresponding correction or retraction notice (example). These practices are in line with the best practices linked in my previous email. JOSS’ current method of adding a comment to the original peer review history thread in Github would not meet PMC’s requirements. Would JOSS consider updating its correction and retraction practices going forward to be in line with best practices?

@xuanxu – can we look at updating our handling of retractions? I think we should do something like this:

On a submission being retracted it should be possible for an EiC to run a follow-up command like @editorialbot retract and pass in a location to a retraction notice. The retraction notice should be a special kind of JOSS paper that doesn't have a software archive. I'm thinking something like this:

• EiC visits original review thread for the paper being retracted and types @editorialbot retract --notice=https://github.com/openjournals/retraction-00001 :point_left: URL being where the retraction notice is stored.
• Editorialbot compiles the paper (pushing branch to joss-papers) and links to preview of paper to be retracted.
• If retraction notice looks OK, EiC does @editorialbot retract --notice=https://github.com/openjournals/retraction-00001 --deposit=true or something like that.
• Editorialbot publishes retraction notice.

Open questions:

• What should the DOI for the retraction notice be? I'm thinking it should be related to the original DOI (e.g., for 10.21105/00001 we could have 10.21105/00001R)
• If the above works, what volume/issue/page number would we use (for volume and issue, I think we just use the normal scheme, but what about page number?)
• What should we do with the original paper? We might want to link it 'forward' to the retraction notice (e.g., similar to https://joss.theoj.org/papers/10.21105/joss.01277) but I'm not completely sure. Let's make sure we follow COPE's guidelines here: https://publicationethics.org/files/retraction-guidelines.pdf

Thank you for providing the direct URLs, however, is there any way for users/readers to navigate to these pages from the journal website, or are these pages only accessible if a user knows the direct URL? Additionally, I noticed that the pages where content is filtered by year appear to display all papers (i.e. also includes pending/non-peer-reviewed papers). When I click the filter for ‘Published papers’ however, it goes back to displaying all papers regardless of year. Is there any sort of table of contents for published/accepted content to facilitate browsing by publication date, volume, or issue?

@xuanxu – can we make some simple views (e.g., lists of linkable titles) that show on a single page all of the papers by issue/volume/year? The existing Rails filters should do most of the work here, but I think PMC is asking for the tables of contents to be easier to discover/browse (e.g., from the navigation menu).

How long can something stay in pending? Do articles ever get the boot from the pending stage?

@chartgerink – I'm not sure I understand the question. Are they asking if articles can be booted out before they go for review? If so, the answer is 'yes'. In fact, about 25-30% of articles stop at this point (see stats in https://blog.joss.theoj.org/2023/05/JOSS-publishes-2000th-paper). This is mostly because of scope reviews and feedback to authors that their submission isn't ready to move forward.

Does the journal have any update policy? Since code bases and technology update overtime, is there an expectation for the articles to be living documents?

We do support follow-up submissions for already-published software, provided the updates meet the same scholarly effort criteria as required in our submission guidelines (https://joss.readthedocs.io/en/latest/submitting.html#submission-requirements). I think this used to be documented somewhere but I can't find it now.

Do you think I should write a short paragraph about this @chartgerink so we can provide an explicit link?

[xuanxu]

@xuanxu – can we make some simple views (e.g., lists of linkable titles) that show on a single page all of the papers by issue/volume/year? The existing Rails filters should do most of the work here, but I think PMC is asking for the tables of contents to be easier to discover/browse (e.g., from the navigation menu).

Sure, I'll draft something

[xuanxu]

• What should we do with the original paper? We might want to link it 'forward' to the retraction notice (e.g., similar to https://joss.theoj.org/papers/10.21105/joss.01277) but I'm not completely sure.

We could add a link to the sidebar on the paper page

[zchandler]

Fan of JOSS here. Is there anything that your supporters can do to help with this? Subscribing.

[chartgerink]

@chartgerink – I'm not sure I understand the question. Are they asking if articles can be booted out before they go for review? If so, the answer is 'yes'. In fact, about 25-30% of articles stop at this point (see stats in https://blog.joss.theoj.org/2023/05/JOSS-publishes-2000th-paper). This is mostly because of scope reviews and feedback to authors that their submission isn't ready to move forward.

@arfon - I think you're correct. Maybe we should document this somewhere as well?

Fan of JOSS here. Is there anything that your supporters can do to help with this? Subscribing.

@zchandler - at this time you cannot support the efforts as we're all in the hands of PubMed Central. We need to resolve the questions pending in https://github.com/openjournals/joss/issues/153#issuecomment-1571562457 but they're primarily things we editors need to fix. Thanks for offering! 😊