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.

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.

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

👍 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?

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

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.

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.

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

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?

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...

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] #153 (comment)

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

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.

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

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

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...

Excellent. Thanks @genomematt!

Many thanks, @genomematt!

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?

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/

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.

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.

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

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

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.