I was recently doing some research on PubMed and I noticed that, in my field of research (plant science), some articles are referenced and others are not, even for two articles in the same journal...

Does everyone know what is (are) the condition(s) for a paper to be listed in PubMed?

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    See ncbi.nlm.nih.gov/books/NBK3827/#pubmedhelp.PubMed_Coverage and nlm.nih.gov/pubs/factsheets/dif_med_pub.html in particular. But wow, was that buried deep. (Ps. Not posted as an answer because a proper answer really should summarize the pages, not just link to them. If anyone wants to do that, please feel welcome.) – Ilmari Karonen Apr 1 '13 at 8:08
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    Because there are non-biomedical research articles? Would you really expect to find physics or economics research papers on PubMed? – JeffE Apr 1 '13 at 22:48
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    @JeffE my filed of research is plant science (I updated the original question) why is not in biomedical research. However, many article in plant science ARE referenced on PubMed, while some are not, even on the same topic... – Wiliam Apr 2 '13 at 7:06
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    @scaaahu you could extend that reasoning to all other questions on this site :) – F'x Apr 2 '13 at 10:59
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    @scaaahu but not the unique source of information. – Franck Dernoncourt Nov 20 '15 at 17:49

Because PubMed is about biomedical literature and life science journals. Things are blurry, however, because of two factors:

  1. Obviously, there is no strict definition of what is (or is not) biomedicine.
  2. PubMed does not select “article by article”, but has a list of indexed journals, from which all papers are indexed. Yet, a single journal's scope can be very varied.

Combine the two, and you get the idea that there is a lot of variability in whether an article on a given topic is published. For example, my own research field is materials chemistry, and about two-thirds of my papers appear to be indexed in PubMed: probably because those were published in generic chemistry journals, which also happen to publish some papers of relevant to life science.

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from here

The National Library of Medicine uses an NIH-chartered committee, the Literature Selection Technical Review Committee (LSTRC), to review all new biomedical and health journal titles and recommend those to be indexed for MEDLINE®. The NLM Fact Sheet titled "MEDLINE Journal Selection" provides information on the role of the LSTRC and critical factors considered in making the decision to recommend a journal title for indexing. It is intended only as a guide since there is no one set of characteristics that will guarantee selection. The LSTRC considers the quality of the scientific content, including originality, and the importance of the content for the MEDLINE audience throughout the world.

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Often there are journals that clearly have bio-medical content, and are not found in PubMed. That's because registering a journal in PubMed is a non-trivial task. Even for big players like Cell Press it took almost a year to put "Cell Reports" in there.

The publisher can apply to be included in PubMed, but that usually takes some time. The meeting where it is discussed if a journal is included is only held twice per year. One requirement is that the journal is also available in print. That's why many journals start with a print issue and then after inclusion in PubMed drop it again.

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Let me start by saying that some of the other answers are misleading because Medline is not the same as Pubmed. You'll find Medline-indexed journals which are selected by LSTRC in Pubmed, but Pubmed also contains other articles from non-Medline indexed journals - hence the answer about LSTRC selecting Medline journals isn't wrong but does not answer the question at hand. If a journal is in Pubmed (e.g. because the publisher submits to PubMed Central, or because it is selected for Medline) then usually ALL articles from that journal are in PubMed. The answer to the mystery why some articles from a journal may be in Pubmed and others are not may have to do with the fact that authors can submit their accepted manuscript to PubMed Central (PMC, which hosts full-text articles) and then they also show up in PubMed. If authors are funded by NIH or other funding agencies they even have a mandate to make their manuscript openly accessible. If the journal is not open access they have to submit it to PMC using the author manuscript submission pathway. The paper will then show up in PubMed, even though the full journal is not Medline indexed.

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