What is PubMed? Is it a search engine? A credentialing system? A filter? Is it a publisher? An enabler of open access (OA) publishing? A technology provider? A competitor? Depending on the situation, you can answer each of the above in the affirmative, despite the contradictions many of the combinations may cause.
Twenty years ago, PubMed was a credentialing system, an online port of the MEDLINE index. This shift of medium quickly made it a search engine, but one built on a manual and highly curated index. If your journal was in MEDLINE/PubMed, it had gone through an exhaustive evaluation, and had earned a badge of legitimacy. You were searching a credentialing system. You were getting filtered results based on MEDLINE inclusion criteria, which were well-accepted.
Starting with E-Biomed and stretching to PubMed Central, the credentialing system pegged in many users’ minds morphed into a publisher (a primary publisher in the case of at least two journals, and, for a time, three), a competitor (here, here, and here, as well as here and here), and a technology provider. Its management also has advanced the cause of OA publishing, in both legitimate and controversial ways. Part of the extension of PubMed’s original purpose has come through brand extension via PubMed Central, which has been used to muddy the waters about what is PubMed and what is not. PubMed inclusion has been used, for example, as an incentive for journals to include themselves in PubMed Central, eroding the idea that PubMed is a neutral arbiter of quality.
Now, a new twist is emerging, and that seems to be that PubMed may be consciously or unwittingly acting as a facilitator of predatory or unscrupulous publishing.
In a paper published in Neuroscience, the authors analyzing the neurology and neuroscience journals included in PubMed found that:
- Twenty-five predatory neurology journals were indexed in PubMed, accounting for 24.7% of all predatory neurology journals.
- Fourteen predatory neuroscience journals were indexed in PubMed, accounting for 16.1% of all predatory neuroscience journals.
- Only one of the 188 predatory neuroscience or neurology journals appeared in the DOAJ index.
- Only 54.6% of the journals deemed predatory in neuroscience actually contained articles.
The authors note how PubMed Central provides a backdoor into PubMed and the National Library of Medicine (NLM) for these predatory publishers:
Noteworthy, predatory journals are retrievable in the catalog of the National Library of Medicine (NLM), are labeled by a unique NLM identification number and referenced as “Not currently indexed for MEDLINE. Only citations for author manuscripts are included.”
This is the kind of fine print that will escape the attention of most users, and which itself is unclear as to reliability, process, or value. Are we to think that something that appears in PubMed and the NLM but not in MEDLINE has some lesser status? The confusion is multi-layered for users.
This study was published in April, but went largely unnoticed until the authors published on 19 August 2017 a letter based on the same research in the Lancet. In this letter, the authors state their recommendations thusly:
Furthermore, although the National Library of Medicine refers to these journals under the descriptor “Not currently indexed for MEDLINE”, citations for author manuscripts are labelled as “included”. Thus, highly regarded databases like PubMed and PubMed Central should raise the bar for journal acceptance, and join the Directory of Open Access Journals, Scopus, and MEDLINE in imposing stringent criteria for inclusion of journals and publishers.
The PubMed database managers have irresponsibly allowed it to become a repository of citations to predatory journal articles. Among other things, the next time you see a questionable journal proudly announcing that it is indexed in Pubmed, chances are that the journal is predatory. Contrary to the popular notion that only genuine and distinguished journals which take peer-reviewing seriously and follow all the norms of scientific publishing are indexed in PubMed, many predatory journals too are included in PubMed. The same holds true for PubMed Central too.
PubMed’s brand has long been muddled in ways that pass lower-quality works through the system under cover of prestige. This has real consequences. A recent article in BusinessWeek outlines how the “predatory” publisher OMICS is being used by pharmaceutical companies to quickly get citations for studies major journals won’t accept and run meetings to push their products.
Despite being caught red-handed publishing “fake science” in Canada, OMICS doesn’t seem fazed. In response, it is running today’s standard playbook built on bluster and bombast, including calling accusations against it “fake news” and its founder claiming implausibly, “We’ve never made a mistake.” Currently the subject of a US Federal Trade Commission prosecution, OMICS:
. . . first got into trouble with the U.S. government in 2011. The National Institutes of Health, a division of the U.S. Department of Health and Human Services banned OMICS journals from indexing in PubMed Central, one of the world’s primary databases for medical research, given “serious concerns” about its practices. In 2013, HHS accused OMICS of trademark infringement and using the names of employees at the NIH and PubMed Central “in an erroneous and/or misleading manner.”
While OMICS is ostensibly banned from PubMed Central, it doesn’t take long to come across the OMICS Journal of Radiology in PubMed and PubMed Central. This again shows what a confusion of journals PubMed has become. One URL you get on the first page of a simple Google search for OMICS in PubMed is “https://www.ncbi.nlm.nih.gov/labs/journals/omics-j-radiol/” with the curious “labs” element in it. At the top of the resulting page, it reads, “A PubMed Lab experiment.” Clicking on this tagline takes you to a blog entry from September 7, 2016, which talks about this new experiment apparently aimed at letting users follow certain journals. It seems like an experiment that never took off, yet a Google search finds the page, an OMICS journal with a full accoutrement of PubMed elements is discoverable, and PubMed citations are easily retrieved.
PubMed’s brand has long been muddled in ways that pass lower-quality works through the system under cover of prestige. This has real consequences.
You may also have caught that the reporters from BusinessWeek were also confused by what PubMed Central is, describing it as “one of the world’s primary databases for medical research.” PubMed describes itself as “a free full-text archive of biomedical and life sciences journal literature.” Yet, you can find articles about quantum chromodynamics (QCD) from the European Physics Journal C, Particles and Fields, in PubMed Central. There are hundreds of entries for astrophysics, many of which seem irrelevant to biomedicine and life sciences. Several US funding agencies also use PMC as their repository, including the Department of Homeland Security and the Department of Veteran Affairs. It seems “biomedical and life sciences” are quite broadly defined by PMC.
Maybe PubMed is confusing even to itself?
In addition to the dubious role of certification databases when it comes to questionable journals, the role of scientists in the predatory publishing phenomenon is the subject of a recent article in Nature by David Moher, Larissa Shamseer, Kelly Cobey, and their colleagues. In their review of nearly 2,000 biomedical articles from more than 200 journals thought to be predatory, more than half of the corresponding authors hailed from high- and upper-middle-income countries using World Bank criteria. This flies in the face of the common assumption that predatory publishers are exploiting desperate authors in low-income countries. More worrying is that of the 17% of the sampled articles that reported a funding source, the NIH was the most frequently named funder. The US itself produced more articles in this sample than any other country save India. The authors note:
Our experience with these journals is that they provide both poor vetting and poor access. Their websites and archiving systems are unstable. Although some articles appear in PubMed (often after a delay), the titles are not indexed by Medline and are difficult to find.
What’s the thread through PubMed over the years since it was ported from MEDLINE? The unifying theme I see is a hunger to adapt. At times, this has been a boon — the port of MEDLINE to PubMed was a smart move, and some interface changes have been commendable. At other times, these adaptations have revealed a clear lack of purpose and mission, such as the controversial involvement with eLife, the competition with publisher brands and traffic, and now the loose standards that have allowed unscrupulous publishers to enter PubMed via PMC.
Adaptation is required to remain relevant, but there have to be limits, or the adaptation may cause the entity to simply dissipate into the environment via entropy. PubMed seems to be giving into entropy. It needs to realize this moment calls for something else — clarity, standards, and credentialing that means something. Their opportunity is not to follow, but to lead.