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 #124. I'll try to submit GeneNetwork once we have those.

[tracykteal]

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]

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]

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

[konrad]

👍 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]

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]

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]

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]

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

[HenrikBengtsson]

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]

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]

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.

[Kevin-Mattheus-Moerman]

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]

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