Add JOSS to pubmed - Githubissues

pjotrp commented 7 years ago

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.

tracykteal commented 7 years ago

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.

genomematt commented 7 years ago

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.

pjotrp commented 7 years ago

The NIH is a funder of both PMC and GeneNetwork. So we should attempt this.

konrad commented 6 years ago

:+1: 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?

kyleniemeyer commented 6 years ago

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

konrad commented 6 years ago

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.

kyleniemeyer commented 6 years ago

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.

konrad commented 6 years ago

That's great! I also assume that the processing of the application might take a while. Many thanks and fingers crossed.

HenrikBengtsson commented 6 years ago

I noticed JOSS is listed on PubMed (https://www.ncbi.nlm.nih.gov/nlmcatalog/101708638) with

In: PubMed: Selected citations only Current Indexing Status: Not currently indexed for MEDLINE. Citations are for articles where the manuscript was deposited in PubMed Central (PMC) in compliance with public access policies. For further information, see Author Manuscripts in PMC.

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?

arfon commented 6 years ago

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...

konrad commented 6 years ago

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).

Dear NLM team,

since very recently the "Journal of open source software" (JOSS) [1] is indexed in MEDLINE/PubMed [2]. Currently, it seems as only one of its article was included to MEDLINE/PubMed (tested using this search [3]). JOSS is an rather open journal and the mentioned problem was raised in a GitHub issue. Could you please answer the following questions either via email to me or directly in the linked GitHub issue threat:

Why is so far only one article indexed in MEDLINE/PubMed?

Will all future JOSS articles be indexed automatically in MEDLINE/PubMed?

Will also JOSS articles be indexed if they were published before JOSS was added to be indexed in MEDLINE/PubMed?

Many thanks in advance.

Best wishes

Konrad Förstner

PS: I wanted to submit this request directly via the PubMed Customer Service form but got always errors (e.g. Error ID 5527bcab-4ff7-47af-94d6-ec827bde41ae).

[1] http://joss.theoj.org/ [2] https://www.ncbi.nlm.nih.gov/nlmcatalog/101708638 [3] https://www.ncbi.nlm.nih.gov/pubmed?term=%22J%20Open%20Source%20Softw%22%5BJournal%5D [4] https://github.com/openjournals/joss/issues/153#issuecomment-337460297

As soon as I get a response I will inform you here.

Kevin-Mattheus-Moerman commented 6 years ago

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.

konrad commented 6 years ago

The automatic email response says that they will answer within 4 business days. I will let you know once I have a proper response.

konrad commented 6 years ago

I received (already some days ago - sorry for the delay) the following response:

The journal you reference, Journal of open source software" (JOSS) is not a
title indexed for MEDLINE. Please see https://www.ncbi.nlm.nih.gov/nlmcatalog/101708638

I would also like to suggest a recording of a webinar we recently held
discussing how journals are added to both PubMed as a MEDLINE journal: https://www.nlm.nih.gov/bsd/disted/video/selection.html

genomematt commented 6 years ago

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...

arfon commented 6 years ago

Excellent. Thanks @genomematt!

konrad commented 6 years ago

Many thanks, @genomematt!

sebastiz commented 6 years ago

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?

federeghe commented 6 years ago

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/

sebastiz commented 5 years ago

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.

arfon commented 5 years ago

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.

@sebastiz - that would be great, thanks! Let me know if you need any help with this.

danielskatz commented 5 years ago

Does one of the editors want to pursue the Clarivate Analytics / Web of Science path mentioned by @federeghe a couple of comments above?

sebastiz commented 5 years ago

Hi @arfon

So the pubmed registration needs to be done by the editors it turns out. The page for submission is here: https://www.ncbi.nlm.nih.gov/pmc/pub/addjournal/

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. The journal must be in scope for PMC, as described in the PMC Scope section of the PMC Policies page. The journal must be able to provide NLM with immediate access to the content at a publisher or third-party site, as required by NLM's Electronic Resources policy. For publishers with at least a two-year history of quality scholarly publishing in the life sciences, a minimum of 25 peer reviewed articles (e.g., original research or review articles, clinical case reports) must be published in final form before you apply.

Can one of the editors submit for ISSN and NLM and then the journal can be submitted

arfon commented 5 years ago

Thanks for digging into this @sebastiz. We already have an ISSN for JOSS. Unfortunately we don't currently doing the following:

A journal must provide PMC with the full text of articles in an XML (eXtensible Markup Language) format that conforms to an acceptable journal article DTD (Document Type Definition) and meets the PMC Minimum Data Criteria. PMC does not accept articles in HTML format.

NLM recommends that data be submitted in XML conforming to the NISO JATS Journal Publishing Tag Set, but PMC will also accept data in other full-text article DTDs that are widely used in life sciences journal publishing.

sivaramambikasaran commented 5 years ago

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...

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.

goerz commented 5 years ago

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.

pjotrp commented 5 years ago

@goerz that should not prevent you from publishing in JOSS. It makes your software citeable while you can still publish methods etc. in other journals. I have no doubt, btw, that JOSS will be indexed in time. With 500 publications JOSS is getting harder and harder to ignore. This is a true outlet of scientific work. Better than many other journals out there ;). Do disrupt with us. Web of Science will wake up to it.

arfon commented 5 years ago

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.

I don't know about PMC progress (I didn't submit the original request), but we're working on adding an ethics statement in #496 which was a blocker for us being indexed in Scopus.

I'm also actively investigating creating JATS XML for JOSS papers which would be necessary for us to be indexed in PMC.

meg-simula commented 4 years ago

[I found this thread when checking if JOSS is Scopus indexed.] What is the current status on this? I noticed that the ethics statement issue was resolved. Is there any remaining issues re: scopus indexing (i.e. anything I can contribute with)?

arfon commented 4 years ago

Is there any remaining issues re: scopus indexing (i.e. anything I can contribute with)?

Thanks for asking @meg-simula. At this point we're waiting to hear back from Scopus. I resubmitted JOSS for indexing about a month ago.

jbloom commented 4 years ago

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.

I don't know about PMC progress (I didn't submit the original request), but we're working on adding an ethics statement in #496 which was a blocker for us being indexed in Scopus.

I'm also actively investigating creating JATS XML for JOSS papers which would be necessary for us to be indexed in PMC.

I was just curious if there is progress on getting JOSS papers indexed by PMC. We'd like to submit to JOSS, but having PMC indexing is important for NIH grants.

iskandr commented 4 years ago

Is there anything us observers can do to help get JOSS indexed by PubMed?

arfon commented 4 years ago

The main issue here is that PubMed needs JOSS to produce JATS XML before they will index us. Unfortunately the Pandoc--JATS conversion is somewhat buggy and I got stuck on this a while ago in https://github.com/openjournals/whedon/pull/45

I definitely want to get this done at some point, it's just hard to find the time to debug the conversion sorry 😞

DominiqueMakowski commented 4 years ago

Happy new year all ☺️

Just came here for some updates about the referencing of JOSS in various databases (unfortunately quite important for many researchers). If I understand the thread correctly:

PubMed: blocker issue (https://github.com/openjournals/whedon/pull/45)
Scopus: pending (submitted in September) - any news on that?
Web of Science: not submitted (?)

arfon commented 4 years ago

Hi @DominiqueMakowski

PubMed: blocker issue (openjournals/whedon#45)

Correct. Although we made a good bit of progress on this last week with https://github.com/jgm/pandoc/pull/6020

Scopus: pending (submitted in September) - any news on that?

I just asked for a status update from Scopus yesterday. Not sure of the status of this but it's still pending.

Web of Science: not submitted (?)

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

DominiqueMakowski commented 4 years ago

Thanks for everything @arfon 🙌

dpole commented 4 years ago

Hi @arfon , is there any update on Scopus/WOS? I have to decide which journal to target. JOSS looks perfect except for this databases issue, which is somewhat relevant to my academic system -- unfortunately :( . I'm happy to contribute, if I can. Thanks for your work!

arfon commented 4 years ago

I’m afraid not sorry. These systems are essential information ‘black boxes’ - we’ve asked to be indexed but we have no way of checking on the status of this request 😔

genomematt commented 4 years ago

Just got this in one of my old mailboxes. Its been quite a while since I suggested it @arfon I have forwarded to your gmail

ISSN / E-ISSN: / 2475-9066 
Publisher: Open Journals 

Dear Dr. Matthew Wakefield, 

The title mentioned above has been evaluated for inclusion in Scopus by the 
Content Selection & Advisory Board (CSAB). The review of this title is now 
complete and the CSAB has advised to not accept the title for Scopus 
inclusion at the present time. For your information, the reviewer comments 
are copied below: 

I really like the concept of a journal publishing software development. 
Usually, software developers get insufficient credit for their work which 
takes significant effort. This negatively impacts on attracting top-level 
PhD students to work on significant software development and on subsequent 
tenure&promotion. Unfortunately though this journal does seem to accept 
most submissions. Reviewing is somewhat limited. So, accepting this into Scopus 
would not be consistent with other journals' acceptance. Rigorous reviewing of 
implementation work guaranteeing highest standards would benefit the entire area 
and allow us to accept such a title into Scopus. 
Unfortunately, the current title does not do this. 

If in the future these comments are addressed, you may decide to submit a new application at any time after the following date: March 2022. 
At that time, you will be required to upload a cover letter detailing how the above comments have been addressed. 

Finally, we strongly advise you to read through our FAQs: 
Helping to improve the Scopus submission & success process for editors and publishers: https://embed.widencdn.net/download/elsevier/olbvgdobzi/SC_FAQ-content-selection-process_Jan2019.pdf?u=simrzc 
Role of an editor: https://www.elsevier.com/__data/assets/pdf_file/0005/95117/SC_FAQ-Role-of-an-Editor-22092014.pdf 

Yours sincerely, 

Scopus Title Evaluation Support 
titlesuggestion@scopus.com

genomematt commented 4 years ago

Note that 12 March 2018 was the submission date https://github.com/openjournals/joss/issues/153#issuecomment-372170246

arfon commented 4 years ago

Thanks @genomematt - I have a bunch of issues with that response from Scopus but am at a bit of a loss how to proceed.

I’ll sync up with the JOSS editorial team and try and figure out what next steps might look like here.

tknopp commented 4 years ago

@arfon I would encourage you to get in contact with Scopus and respond to their review. Question is whether you can derive some acceptance rate for JOSS. That would be helpful in the response.

arfon commented 4 years ago

@arfon I would encourage you to get in contact with Scopus and respond to their review. Question is whether you can derive some acceptance rate for JOSS. That would be helpful in the response.

Thanks for the encouragement @tknopp. We will do this at some point and we've discussed how we can derive an acceptance rate based on the papers we have rejected as out of scope or not up to standard.

Do you have any contacts at Scopus? The reassessment every ~2 years is a little frustrating, especially when they seem to have misunderstood how JOSS functions.

Oftatkofta commented 3 years ago

Hi all,

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

tknopp commented 3 years ago

I forgot to answer to @arfon. No, I do not have a more direct contact to scopus but I have successfully landed another journal in scopus (https://journal.iwmpi.org) and went through the registration process.

From my perspective the most important thing is to derive rejection / out of scope metrics. Once that is in place it should be relatively straight forward to write a good response to the initial review. The most important thing to think about is whether an open review model leads to the situation that more "low-quality" paper are accepted since nobody wants to raise critical points in public. This issue for open review models needs to be discussed and it needs convincing arguments and examples, how this issue is resolved. On the pro side one can then also list all the positive aspects of open review models but critical reflection on the issue raised by the scopus reviewer certainly raises the chances to get listed.

danielskatz commented 3 years ago

I think there's a fundamental problem here if one of the SCOPUS criteria is acceptance rate, given that our goal is to collaboratively improve submissions to the point where they become acceptable, not to reject them.

tknopp commented 3 years ago

I fully agree with that. But still it would be interesting to see some numbers about the acceptance rate to discuss the issue raised by the reviewer. If its 100% acceptance rate one would answer differently to Scopus than if the acceptance rate is 50%.

danielskatz commented 3 years ago

I would guess it's around 80%, mostly based on some rejected before review (or in review) as being out of scope, typically having insufficient work/contribution, and a very small number rejected because the changes needed are more than the authors want to do. @arfon and @csoneson - would either of you have a way to figure this out?

csoneson commented 3 years ago

I can find 137 pre-review issues and 12 review issues that were opened in 2020 and have the 'rejected' label attached. In total, 547 pre-review issues and 391 review issues were opened in 2020.

tknopp commented 3 years ago

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.

openjournals / joss

Add JOSS to pubmed #153