How to Get Your Articles Indexed in PubMed: The Go-To Guide for Publishers
PubMed Indexing XML

How to Get Your Articles Indexed in PubMed: The Go-To Guide for Publishers

Shanu K
Shanu K
PubMed-Indexing-Typeset-Resources

For journals in the medical and life sciences space, getting indexed in PubMed is a high priority goal. However, no clear resource exists that gives a step by step run-through of the process that will get your articles indexed in PubMed. We intend to remedy that with this blog post. A complete link of resources for further reference is appended at the end of this post.

PubMed, developed and maintained by the National Center for Biotechnology Information (NCBI) at the National Library of Medicine (NLM), is a free resource that provides public access to:

  • Citations and abstracts in the fields of medicine, veterinary medicine, nursing, dentistry, preclinical sciences and healthcare systems from MEDLINE (more about MEDLINE later). Also available are citations for most books on the NCBI bookshelf.
  • Links to full-text articles from PubMed Central (PMC), other publisher websites and related resources.

The two-pointers above are heavily summarized and the actual scope of PubMed is more detailed. While it is largely a database of content in the medical and biological sciences, it does include citations and links to some out-of-scope journals — primarily general chemistry and general science journals.

Benefits of Getting Indexed in PubMed

A lot of people talk about getting indexed in PubMed, however, you don’t really apply to ‘get indexed in PubMed’ (we’ll see why in the next section that differentiates PubMed, and PMC). However, if links to your articles or citations and abstracts from your journals become searchable in PubMed’s database, the benefits are primarily twofold:

  • It increases trust in your journal’s processes and commitment to science. This makes it easier to attract quality submissions. Of course, PubMed has been in the news several times for including links to predatory journals and dubious content, but on the whole, showing up on PubMed is considered a certification of quality.
  • Increases exposure. As with most good indices, getting indexed in PubMed leads to an increase in the reach and exposure of your journal. This not only increases the traffic to your journal’s website and articles, but is also a precipitating factor for an eventual increase in citations and impact factor.

Before we get started with the process of getting your articles in PubMed, there’s a primary distinction that needs to be understood.

Difference between PubMed and PMC

PubMed is a searchable database of citations and abstracts. To show up in search results on PubMed your journal needs to be submitted to either MEDLINE or PMC or both. There is no application for PubMed — citations, abstracts, and links to full-text articles are pulled from MEDLINE, PMC, and the NCBI Bookshelf.

PMC was launched in 2000 and is a free archive for full-text articles in the biomedical and life sciences space. It serves as a repository for journal content deposited by participating publishers. PubMed recommends all journals to submit full-text articles to PMC and the application guidelines are less strict than for MEDLINE. Of course, journals can apply for both PMC and MEDLINE — but rejection from one may affect your application’s acceptance for the other as well.

Getting Indexed in PMC

If your journal is accepted in MEDLINE, you can expect to be accepted to PMC as well. It is a free archive and works well with MEDLINE’s requirements for electronic-only journals. However, if you submit to PMC and are rejected, then you cannot submit to both PMC or MEDLINE for the next two years.

Mandatory requirements for inclusion in PMC

  1. The publisher should have a two-year history of quality scholarly publishing the biomedical or life sciences fields. In some cases, a one-year history may be considered for review.
  2. Journal must have a registered ISSN.
  3. The journal must be able to provide NLM with immediate access to its content in accordance with NLM’s Collection Development Guidelines.
  4. The journal must have published at least 25 peer-reviewed articles.
  5. The journal needs to meet PMC’s language guidelines.
  6. The journal primarily consists of one or more of the following types of content: original research and review articles, clinical case reports, data descriptor articles that point to a dataset, and descriptions of clinical or surgical procedures.

If you meet these requirements, you are eligible to fill in the application form.

Filling the Application for PMC

The application form for PMC needs to be filled in through the PMC Publisher Portal. Similar to MEDLINE, you will be asked for contact details as the first step. Be sure to add in an email address that is regularly monitored.

PubMed-Indexing_Application-Submission
Source: https://www.ncbi.nlm.nih.gov/pmc/pub/addjournal/

What happens next

Once received, NLM will conduct an initial screening of your application against the mandatory requirements listed above. If your application fails at this stage, you can reapply only after 2 years.

After the initial screening, your application moves to the Scientific Quality Review stage where PMC evaluates the journal information, policies and content. If your journal fails to at this stage, you will be deemed ineligible to reapply before 2 years are up. Read more about the scientific and editorial quality assessment by PMC.

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

If you pass the above two assessments, you then move to the Technical Evaluation stage. At this point, you will be asked to fill out a technical evaluation checklist and submit a set of sample files for 25 articles. The files to be deposited for each article include:

  • A separate XML data file for the full text of each article. To generate the XML, you can use from a variety of online sources. (e.g. Typeset’s PMC XML generator is built for that purpose)
Typeset-PMC-XML-Converter
Typeset’s MS-Word to PMC XML converter (Source: https://www.typeset.io/for-publishers/convert/word-to-pmc-xml/)
  • High-resolution, original digital image files for all figures in each article.
  • A PDF, if one exists, in addition to the XML version (but not as the only form).
  • Supplementary material files (e.g., spreadsheets or video files) available with the article. (See Supplementary Material policy)

All sample files have to meet the minimum data criteria set out by PMC. This is mandatory. Failure to meet it will result in rejection. Files will also be evaluated on the accuracy of presentation and adherence to Delivery specifications.

Once you pass the technical evaluation stage, your journal’s as good as accepted as you move into the Pre-Production stage. In this stage, you will submit a PMC Participation Agreement. There are three different types of agreements, you will need to choose the one you are eligible for. Read more about Participation Agreements and Options.

In the Pre-Production stage, you will also submit a complete set of article files that meet PMC’s Back Content Policy and journal banner images that match PMC’s banner specifications.

PMC will review the Participation Agreement, perform QA checks on the content files and send you a preview version of your journal’s PMC site. If there are repeated or serious errors in your content files, your journal could be rejected at this stage.

Passed them all? Time to go live!

PMC now countersigns the Participation Agreement and releases the journal to PMC’s public site.

You are in.  

...

Before you exit,

Complete List of Resources

General Resources

Typeset.io: For automatically generating PMC compliant article XMLs.

Difference between MEDLINE, PMC, PubMed

Recommendations for the Conduct, Reporting, Editing, and Publication of Scholarly Work in Medical Journals from ICMJE — http://www.icmje.org/icmje-recommendations.pdf

Principles of Transparency and Best Practice in Scholarly Publishing (joint statement by COPE, DOAJ, WAME, and OASPA) — https://doaj.org/bestpractice

Get-indexed-in-PubMed
Source: http://www.den.org.au/resources/

Getting Indexed in PMC: Resources

How to Include a Journal in PMC
FAQs for Publishers
Journal Selection
PMC policies
Participation Agreements and Options
File Submission Specifications
Publisher Portal

Appendix:

If you found the above article interesting, the following blogs might also interest you.

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  3. JATS XML: Everything a Publisher Needs to Know
  4. Top 5 Reference XML Generation For Academic Publishers