Add JOSS to pubmed #153
Comments
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I agree it would be great to get articles indexed in PubMed and is important for bioinformatics in particular. It's unlikely the journal will get in through the MEDLINE journal selection process, since it's not biomedically focused. https://www.nlm.nih.gov/pubs/factsheets/j_sel_faq.html However, it seems that if journal or paper content is put into PubMed Central they will be indexed in PubMed, so perhaps we could try that route? http://www.ncbi.nlm.nih.gov/pmc/about/faq-pub/ There is a 'scientific quality standard' there that evaluates " whether the scientific and editorial character and quality of a journal merit its inclusion in PMC". @pjotrp it would be great if there was a test paper you could try this with. |
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The slight issue with the submitting directly to PubMed Central is that it requires the work having been supported by a PMC supporting funder if the Journal is not part of PMC. |
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The NIH is a funder of both PMC and GeneNetwork. So we should attempt this. |
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👍 I would strongly support this suggestion. I have a piece of software that I would like to publish in JOSS but my collaboration partner would like to have it in a journal that is listed in Pubmed. Has there been any attempt to talk to NIH? |
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We could try submitting for MEDLINE review—we do have plenty of biomedical-related articles: https://wwwcf.nlm.nih.gov/lstrc/lstrcform/med/index.html |
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Sounds good and I think this is likely to work. Who of JOSS would be in the position to submit this application? @arfon? Sorry for being pushy. |
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I have been sort-of taking the lead on these indexing efforts, mainly with Google Scholar so far, so I can do this—perhaps tomorrow. Not sure how long it will take to get a response, though. |
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That's great! I also assume that the processing of the application might take a while. Many thanks and fingers crossed. |
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I noticed JOSS is listed on PubMed (https://www.ncbi.nlm.nih.gov/nlmcatalog/101708638) with
I also noticed that there is exactly one JOSS paper indexed there. Is this because JOSS just got added, or what caused that paper to get indexed and not others? Will all future JOSS paper be indexed automatically? |
I'm afraid I don't know the answer to this question. PubMed is outside my area of expertise... |
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I hope this is okay for everybody but I am very interested in the proper indexing of JOSS in MEDLINE/PubMed. Due to that I sent the following request to the NCBI Help Desk (the PubMed Customer Service did not work for me).
As soon as I get a response I will inform you here. |
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Thanks for doing this. We'll see how they reply. If you do not hear anything soon we might follow up with an inquiry directly from the JOSS editorial team (I'll discuss this) as this might have more momentum. Also feel free to ask us in the future to help draft/format messages like this. |
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The automatic email response says that they will answer within 4 business days. I will let you know once I have a proper response. |
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I received (already some days ago - sorry for the delay) the following response:
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I have gone through the process of suggesting JOSS for SCOPUS. The tracking nr. for this title suggestion is: 46B06F641F8C7575. The time line for this is 6-12 months... |
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Excellent. Thanks @genomematt! |
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Many thanks, @genomematt! |
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If you want to submit manually to google scholar by the way then its pretty straightforward. Follow here:...http://blog.impactstory.org/make-google-scholar-better/ I still think its really important to have the pubmed addition especially given the explosion of bioinformatics and R..This would be a real deal-breaker for the use of the rOpenSci pipeline. Any further developments in this? |
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Another interesting place is Clarivate Analytics, the company maintaining Web of Science. This is the submission form if someone wants to try (the submitter must be an editor): http://mjl.clarivate.com/journal-submission/form/ |
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Hi all. Is there an action plan to take Pubmed/JOSS issue forward? Is it just a case of someone submitting an application to Pubmed as per @konrad above . I'm happy to do this if needed. |
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Does one of the editors want to pursue the Clarivate Analytics / Web of Science path mentioned by @federeghe a couple of comments above? |
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Hi @arfon So the pubmed registration needs to be done by the editors it turns out. The page for submission is here: Basically before submission the following needs to happen: The following requirements must be met before making any kind of application to PMC: The journal must have a properly registered ISSN. This means that there must be a confirmed record for the journal in the official Register of the ISSN International Centre. Can one of the editors submit for ISSN and NLM and then the journal can be submitted |
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Thanks for digging into this @sebastiz. We already have an ISSN for JOSS. Unfortunately we don't currently doing the following:
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Any progress on this? Also, will the already submitted publications also be considered scopus indexed. Sorry if the question is stupid, just that I am ignorant of the entire process. |
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I've had a PI shoot down the suggestion to publish in JOSS because it's not indexed by Web of Science. It would be really great if that could change. |
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Did they get back to you at all? |
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@iskandr I will post here as we progress throughout. I have no information as of this point. |
Just a brief update to say that we've just resubmitted JOSS to Web of Science. |
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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
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@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
Open questions:
@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).
@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.
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? |
Sure, I'll draft something |
We could add a link to the sidebar on the paper page
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Fan of JOSS here. Is there anything that your supporters can do to help with this? Subscribing. |
@arfon - I think you're correct. Maybe we should document this somewhere as well?
@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 #153 (comment) but they're primarily things we editors need to fix. Thanks for offering! 😊 |
We have now a Table of Contents page where papers can be browsed by year/volume/issue: https://joss.theoj.org/toc |
Any updates on Web of Science? It appears that JOSS is still not listed in their master list, which could become an issue for me personally, as my employer only considers WoS-indexed publications in our annual salary review process. |
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@chadagreene as an editor of JOSS and person responsible for this issue, I recommend you open up a separate issue to keep track of the WOS indexation discussion. |
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Just documenting an update from our updated submission to PMC, dated Nov 8th, 2023:
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@chartgerink -- I know it hasn't quite been 16 weeks yet, but I'm curious if they sent anything since the first message. |
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@iskandr still awaiting their response - it is due end of month and I'll post back once I know more 😊 |
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@chartgerink relevant to this thread & #1283 the International Science Council invited me to write a piece on JOSS and journal indexing. They've now published it here: https://council.science/current/blog/open-science-round-up-january-2024/ In the final copy-editing ‘research software’ has been changed to ‘software research’ (doh!), I'm trying to get this changed, but otherwise it accurately reflects my views: TL;DR JOSS is awesome and academia needs to think long and hard about the meaning or lack-thereof(!) of Scopus & Web of Science indexing. |
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Hi all - I am relaying a response from Pubmed that I received fifteen minutes ago:
There are still next steps to realize the deposit, but we passed a big administrative hurdle! 🥳 |
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Thanks @chartgerink for pushing this through!! |
Woo hoo! 🎉 |
I have a JOSS manuscript in preparation, and I wanted to see if it was indexed in PubMed and did a quick search for the journal in PubMed a few months ago: https://pubmed.ncbi.nlm.nih.gov/?term=j+Open+Source+Softw%5Bjournal%5D I only glanced it and saw a longish list of papers (I didn't actually check the number), so I assumed it was already indexed, so thought - great, it's indexed in PubMed - I'll submit to JOSS. Recently, I was a looking at the list bit more carefully and then I noticed that there only 68 papers in that list, which seemed too few given the total number on the journal website (but definitely up since this 2017 thread!). I took a look and saw all of them were author manuscripts submitted in PMC (mainly from govt. agencies or HHMS) - not deposited directly by the journal. This lead me to this thread. So I'm happy that it will be more automatically eventually! In the meantime, since I think a lot of people will be put off by non-automatic indexing in PubMed, they should know that as a temporary workaround, one way to get a JOSS paper indexed in PubMed is to submit it directly as an author manuscript via the "NIH Manuscript Submission System": https://www.nihms.nih.gov/login/?next=/submission/ . That's what I intend to do, if the direct deposition isn't up and running by then. I have submitted author manuscripts before and it normally works great. Meanwhile - I'm very happy that JOSS is on this path to being in PubMed automatically! And I'm be happy to help in testing the deposition workflow if you need it. Diamond open-access is the future! |
Does anyone know what the current status of automatic deposition in PMC is? I just got a paper accepted in JOSS, so I'm probably going to submit it via NIHMS as I described above, since I'm not seeing new papers being added yet. But if it's about to start then I can hold off (I assume if and when automation deposition starts it will detect existing entries and not create see duplicates?) |
Argh! I spoke too soon. I started the NIHMS submission and got all the way to the end, and then got this:
In our case, there are no federal grants to add, so it appear that this route to deposition PMC is not available unless there is a federal grant. So that leaves out work that is self-funded, even if it's peer-reviewed and in a journal that is approved to submit. I have written to NLM to get clarification. In the meantime that stinks, since it seems to cut off any direct submission work that although published in a peer-reviewed journal, if the journal isn't already in PubMed and also isn't funded off a federal grant, then it won't be indexed/deposited. That could represent a sizeable scientific work that is being missed. |
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Yesm, I had a similar problem because my work was funded by a Dutch
institution. Putting in your own work is only possible on some limited
number of grants in the USA only.
…On Thu, Jul 18, 2024 at 10:23 PM Alex Lancaster ***@***.***> wrote:
In the meantime, since I think a lot of people will be put off by
non-automatic indexing in PubMed, they should know that as a temporary
workaround, one way to get a *JOSS* paper indexed in PubMed is to submit
it directly as an author manuscript via the "NIH Manuscript Submission
System": https://www.nihms.nih.gov/login/?next=/submission/ . That's what
I intend to do, if the direct deposition isn't up and running by then. I
have submitted author manuscripts before and it normally works great.
Does anyone know what the current status of automatic deposition in PMC
is? I just got a paper accepted in *JOSS*, so I'm probably going to
submit it via NIHMS as I described above, since I'm not seeing new papers
being added yet. But if it's about to start then I can hold off (I assume
if and when automation deposition starts it will detect existing entries
and not create see duplicates?)
Argh! I spoke too soon. I started the NIHMS submission and got all the way
to the end, and then got this:
image.png (view on web)
<https://github.com/user-attachments/assets/2f96135a-bb58-4abf-8cf5-be7bb1fa389a>
In our case, there are no federal grants to add, so it appear that this
route to deposition PMC is not available unless there is a federal grant.
So that leaves out work that is self-funded, even if it's peer-reviewed and
in a journal that is approved to submit. I have written to NLM to get
clarification. In the meantime that stinks, since it seems to cut off any
direct submission work that although published in a peer-reviewed journal,
if the journal isn't already in PubMed and also isn't funded off a federal
grant, then it won't be indexed/deposited. That could represent a sizeable
scientific work that is being missed.
—
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Not finding the checklist that @chartgerink posted in the slack on here, i'll delete if it's somewhere i'm not seeing: Specifically, can we set up a repository that mirrors joss-papers but is adjusted to meet the PMC criteria? For example, a joss-paper-pmc repo that follows the naming and delivery specs from PMC directly. The primary differences are that we need to do some renaming/reorganizing per paper. The specific action items I would see based on my evaluation are:
Also @tarleb mentioned some issues in https://github.com/openjournals/inara and I see some closed but not sure the status of that. |
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@alexlancaster we're still working on getting everything up to PMC's specs - they are particular in their requirements so it is taking a moment. Note As a general rule: If I don't post updates on PMC's correspondence, there are no updates. Thanks @sneakers-the-rat for the copy over here! |
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I've gotten started on this over here: https://github.com/sneakers-the-rat/joss-papers-pmc it turns out that it's not so trivial as we would have hoped since there have been a number of errors so far from inconsistent/incorrect metadata, i'm raising those as I go over in https://github.com/openjournals/joss-papers Since I'm assuming we'll want this to be auditable, i've started making a reproducible series of steps over here so ppl can check my work (and also if you want to contribute then that's np i can make you a collaborator on the repo) along with some logs as i do the steps: https://github.com/sneakers-the-rat/joss-migrate-pmc |
Happy to help with testing. I'll have some time starting in September. |
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ha, @sneakers-the-rat our ways crossed again -- happy to see recent activity to get automated submissions from JOSS to PMC, since now a colleague demands me to upload our recent paper there MANUALLY! ;) |
and others
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 #124. I'll try to submit GeneNetwork once we have those.
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