Be Careful Using NCBI Databases as Journal Whitelists

The logo for NCBI, the National Center for Biotechnology Information.

The logo for NCBI, the National Center for Biotechnology Information.

In this blog post, I will describe and critically analyze four NCBI (National Center for Biotechnology Information) databases and advise which should and should not be used as journal whitelists. The databases are Medline, PubMed, PubMed Central, and the NLM catalog.

Some predatory publishers make misleading claims about the NCBI databases and use their inclusion in them as a mark of legitimacy or approval by the U.S. Government. These claims should be viewed skeptically. There is only one database among the four that can reliably be used as a whitelist.

OMICS PubMed Central

Example of a predatory journal displaying the PubMed Logo (and other logos) to make it appear legitimate.

  1. Medline: Medline is NCBI’s most exclusive list of journals, and scholarly authors can use it as a whitelist when considering which journals to submit their research manuscripts to. It currently contains 5,626 journals. A committee vets candidate journals using a scoring sheet that evaluates several aspects of journal quality, and high-scoring journals are included in Medline. There is no published list of Medline journals. Instead, the journals can be identified by searching the NLM Catalog.


  1. PubMed: PubMed includes Medline abstracts plus abstracts for a diversity of articles published by journals not indexed in Medline. “Medline plus” other entries is not the same as Medline. Inclusion in PubMed often merely means that a journal contains one or more articles funded by the U.S. National Institutes of Health or another government agency, or that the journal has volunteered to make one or more of its full-text articles available for free through PubMed Central. (PubMed is an abstract database and does not contain full texts.)


  1. PubMed Central: PubMed Central (PMC) is a full-text database that is essentially a disciplinary repository for the biomedical sciences. (This database also functions as the publisher of at least one journal.) Just about any publisher can choose to upload their articles to PMC if they are willing to make the articles open access. Many of the articles contained in the database duplicate articles already published in open-access journals. Others are articles that have been added by authors who have federal funding and must make their work publicly available within a year or two after publication. PMC entries are not vetted for quality, so the database should not be used as a whitelist for scholarly authors.
The United States National Library of Medicine. (Photo by Sage Ross).

The United States National Library of Medicine. (Photo by Sage Ross).

  1. NLM Catalog: This online library catalog serves the patrons of the National Library of Medicine. It catalogs books, journals, and other resources. As a library catalog, its function is to help library patrons discover and access information the library makes available or links to. A journal’s inclusion in this catalog does not necessarily reflect on the journal’s quality, and this database should not be used as a journal whitelist. Journals included in the NLM Catalog are marked as being “Currently indexed for MEDLINE” or “Not currently indexed in MEDLINE.”

Together, the NCBI databases freely provide much valuable metadata and scientific research articles, yet their architecture creates much confusion.

None — including Medline — is designed or intended to serve as a whitelist of approved journals for authors seeking high quality publishing venues. Medline functions for some as a journal whitelist, but this use is “off label,” and some journals with questionable editorial practices may slip through this review process. Importantly, the “inclusion” of a journal in the PubMed Central article repository is not a stamp of approval from NIH or any other entity.

Researchers should be suspicious of any journal that displays logos from PubMed or PubMed Central or makes claims about being included in an NCBI database in an attempt to make the journal appear legitimate.

10 Responses to Be Careful Using NCBI Databases as Journal Whitelists

  1. Ahmed says:

    Pubmed is used as the measure for journals credibility and I don’t think this can be changed

  2. Ahmed says:

    Can we consider the following list is the white list?

  3. Scholar SP says:

    You are right:
    “The “inclusion” of a journal in the PubMed Central article repository is not a stamp of approval from NIH or any other entity.”
    PubMed and PMC are fairly repositories that index journals.
    It is also true for the impact factor;
    “The assignment of an impact factor to a given journal is not a stamp of legitimacy or quality”.
    As PubMed is primarily a medical repository, there are hundreds of journals in non-medical fields (physics, maths, geo,…etc) that are not indexed in PubMed. Consequently, PubMed cannot be the lone landmark for legitimacy, otherwise journals in other fields than the medical, are not legitimate, which is of course untrue and senseless.
    As far as I know, editors or publishers should pay to get their journals indexed in PubMed (please correct me if this is not the case), in addition to other criteria required for the inclusion in PubMed, So, in many cases the inclusion of journals in PubMed and PMC might be biased as is the case for many open access journals where money is the the main goal.
    Neither PubMed nor the impact factor is a gauge of quality or legitimacy, though it is a good indicator. It is rather the ethical conduct and the rigor that should matter, not PubMed inclusion, nor the impact factor, ISSN, or DOI that make a journal legitimate or commendable.


    • Christopher Cole says:

      Publishers and editors do not pay to get their journals indexed in PubMed. The cost of indexing is borne entirely by the National library of Medicine (NLM). NLM unlike the Library of Congress is not a copyright depository so NLM also pays for the subscriptions to the journals that they index.

      Further neither NLM nor any other federal library is in the business of creating white lists of quality journals. To do so is to confer an endorsement on a specific business and that by policy is not a role that the federal government assumes.

      Mr Beall has done a fine job of delineating the difference in the 4 products/services offered by NLM. They were designed and built for different purposes but they all share a common trait that they are not “whitelists” or vehicles to endorse specific publications.

  4. Ghazal says:


    Thomson Reuters list will become obsolete within few years. Use Scimago list and choose Q1 and Q2 journals. Presently, there are many journals listed on Thomson Reuters list, which are not considered as good journals. For example, South African Journal of Industrial Engineering is in this list and if you look at the articles, you will see that it has no good content. Impact factor is also another issue, which will become obsolete within few years. The reason is because in calculation of impact factor, two high quality and low quality journals are given equal weights but in SJR index prepared by Scimago, the relative importance of each journals is considered. The monopoly of ISI has already been broken and most universities focus on Scimago ranking.

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