Retraction Watch

Tracking retractions as a window into the scientific process

Widely used U.S. government database delists cancer journal

with 25 comments

The U.S. government biomedical research database MEDLINE no longer includes a cancer journal with a storied past.

Starting August 2017, researchers looking up journals indexed in MEDLINE (which is accessed via PubMed) could no longer find new articles published by Oncotarget, once included on the now-defunct list of possibly predatory journals compiled by librarian Jeffrey Beall.

Joyce Backus, the National Library of Medicine’s Associate Director for Library Operations, declined to say why Oncotarget had been deselected from MEDLINE:

[Oncotarget has] the feedback from the review committee, and they can choose to share that or not…but we don’t share the scientific review by the experts.

However, Backus added, readers who are familiar with the guidelines MEDLINE follows when deselecting journalscan draw their own conclusions.”

Here is some background information from MEDLINE:

Journals may be deselected from MEDLINE for various reasons including, but not limited to, extremely late publication patterns, major changes in the scientific quality or editorial process, and changes in ownership or publishers.

Backus added that since she’s worked with MEDLINE over the past few years, only “a handful” of journals have been removed from the index.

It’s not very many. It’s infrequent.

Oncotarget has been on our radar for some time. Besides a handful of retractions that we’ve covered, we’ve obtained emails that show an editor of the journal, Mikhail Blagosklonny, contacted colleagues of Jeffrey Beall at the University of Colorado Denver who had published in Oncotarget in 2015 after Beall added the journal to his (now inactive) list of possibly predatory publications. In a series of emails, Blagosklonny told the researchers that Beall had tipped him off that their work might be fabricated, and Oncotarget was going to have to retract their papers. Eventually, Blagosklonny withdrew his retraction threats.

PubMed vs PubMed Central

We contacted Oncotarget and received a reply from Ryan Jessup, the Director of External & Legal Affairs for Impact Journals, which publishes Oncotarget. Jessup asked us to email questions; we sent seven, including a question about the editor threatening to retract papers by colleagues of Jeffrey Beall.  We haven’t gotten a response from Jessup, but a spokesperson for the publisher told us:

As of August 2017 Oncotarget is not currently indexed in MEDLINE. However, all content from the launch of the first Oncotarget issue in May 2010 through Volume 8 Issue 30 remains.

Moreover, Oncotarget content continues to be indexed in PubMed and PubMed Central as well as ISI/Web of Science: Science Citation Index Expanded, Scopus, Biological Abstracts, BIOSIS Previews, and EMBASE. 

In addition, in cooperation with the National Library of Medicine, Oncotarget is working towards its goal to submit an entire issue with full text papers (not just abstracts) to PubMed just days after online publication.

We are right now in the process of understanding and addressing MEDLINE comments. Please note that overall MEDLINE comments about Oncotarget are very positive.

Quote: “This journal continues to play a major role in the publication of important basic science research papers. Editorial practices are consistently high. Ethical guidelines are consistently followed. This is an important research journal for the field.”

As we all, including  Retraction Watch, are working on making the publishing industry better and ready for the challenges of the 21st century, Oncotarget continues to make all efforts to meet the highest standards of the industry.

Note: If you’re confused about the difference between MEDLINE, PubMed, and PubMed Central, you’re not alone. Check out this handy guide from the National Library of Medicine, which explains that PubMed includes references from other databases besides MEDLINE, and PubMed Central is a repository for free full-text papers, such as from open-access journals like Oncotarget.

On September 5, a user on Wikipedia deleted the following line from the entry about Oncotarget:

Oncotarget is no longer indexed in MEDLINE, and the last volume to be included is volume 8 issue 30, 2017.

The entry notes:

The information is misleading as the journal is and will be indexed on PubMed. In general, Abstracting/Indexing category states indexes that cover the journal, not hundreds of indexes that do not. The previous statement was not cited.

Qcist.com, which also wrote about the MEDLINE deselection, corrected its original post to explicitly note that new issues of the journal will still be accessible on PubMed.

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Written by Alison McCook

October 25th, 2017 at 2:15 pm

Comments
  • Kent Anderson October 25, 2017 at 3:17 pm

    For more on the confusion of MEDLINE, PubMed, and PMC, see this Scholarly Kitchen post: https://scholarlykitchen.sspnet.org/2017/09/07/confusion-journals-pubmed-now/

    • Stephen Johnsn October 25, 2017 at 5:08 pm

      Unfortunately, that article expresses confusion about these three entities and adds to it by not making the distinctions that are straightforward. MEDLINE is a subset of PubMed, distinguished by MEDLINE records being indexed with MeSH, and is searchable through many interfaces other than PubMed. Basic citation data is not “indexing.” Indexing is the act of adding controlled vocabulary to citations to describe the concepts expressed in the article. MEDLINE does indeed act as quality gatekeeper by maintaining standards for journals that are indexed. MEDLINE records are easily separated from non-MEDLINE PubMed records by using the MEDLINE subset [sb] or searching with MeSH. PubMed Central is an entirely different entity. Poor “branding” perhaps, but that’s a separate issue.

  • From Morocco October 25, 2017 at 3:45 pm

    The study “South African-authored articles in predatory journals” include Oncotarget as a probably predatory with strong evidence (Table 3: Classification of ‘predatory’ papers by journal (2005–2014)).
    Oncotarget is not listed in DOAJ (Directory of Open Access Journals).

    Mouton J, Valentine A. The extent of South African authored articles in predatory journals. S Afr J Sci. 2017;113(7/8), http://dx.doi.org/10.17159/sajs.2017/20170010

  • Stephen Johnsn October 25, 2017 at 4:39 pm

    Oncotarget does not “continue to be indexed in PubMed and PubMed Central…” An indexed PubMed citation is by definition a MEDLINE record. PubMed Central is a repository and does not provide indexing. Non-indexed citations from Oncotarget will “still be accessible on PubMed” but that’s not the same as “new issues.” New issues will be available in PMC, the repository. These distinctions are important!

  • Michael Hoffman October 25, 2017 at 6:30 pm

    > we don’t share the scientific review by the experts

    Would they be subject to a Freedom of Information Act request?

  • Nahhf October 25, 2017 at 11:35 pm

    Too bad, there are some good papers there. I feel like Beall’s list has done more harm than good.

    • Labrat October 26, 2017 at 1:57 pm

      In the same vein, all studies wherever published should be scrutinized. Too often, publication in a certain journal is taken as an absolute sign of quality.

    • ferg November 6, 2017 at 5:29 am

      Its the predatory journals that are doing the harm, don’t shoot the messenger. In these days of fake news public belief in science is ebbing, clouding the waters with non-peer reviewed articles (as has been the case in oncotarget) will further this alarming trend. In fact supplying support to in the uninformed that science cannot be trusted. Its unfortunate that some decent work has been published there, but for the good of both the scientific and layman communities these journals need to be highlighted as suspect as early as possible.

  • fernando pessoa October 26, 2017 at 6:34 am

    Aging (Albany NY). 2010 Dec;2(12):924-35.
    DNA damaging agents and p53 do not cause senescence in quiescent cells, while consecutive re-activation of mTOR is associated with conversion to senescence.
    Leontieva OV1, Blagosklonny MV.
    Author information

    1
    Department of Cell Stress Biology, Roswell Park Cancer Institute, BLSC, L3-312, Elm and Carlton Streets, Buffalo, NY 14263, USA.

    https://pubpeer.com/publications/381E45BF073AC1682CF06077702E80

  • fernando pessoa October 26, 2017 at 6:36 am

    Cancer Res. 2004 May 15;64(10):3653-60.
    Flavopiridol induces p53 via initial inhibition of Mdm2 and p21 and, independently of p53, sensitizes apoptosis-reluctant cells to tumor necrosis factor.
    Demidenko ZN1, Blagosklonny MV.
    Author information

    1
    Brander Cancer Research Institute and Department of Medicine, New York Medical College, Valhalla, New York, USA.

    https://pubpeer.com/publications/FF5B00A0F09A6D4880D97E9010BF47

  • fernando pessoa October 26, 2017 at 6:37 am

    J Clin Invest. 2000 Feb;105(4):533-9.
    Pretreatment with DNA-damaging agents permits selective killing of checkpoint-deficient cells by microtubule-active drugs.
    Blagosklonny MV1, Robey R, Bates S, Fojo T.
    Author information

    1
    Medicine Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.

    https://pubpeer.com/publications/F9E3828272C0BDDA55DAEB7A1AF82E

  • fernando pessoa October 26, 2017 at 6:38 am

    Oncogene. 2001 Jun 28;20(29):3806-13.
    Low concentrations of paclitaxel induce cell type-dependent p53, p21 and G1/G2 arrest instead of mitotic arrest: molecular determinants of paclitaxel-induced cytotoxicity.
    Giannakakou P1, Robey R, Fojo T, Blagosklonny MV.
    Author information

    1
    Medicine Branch, National Cancer Institute, NIH, Bethesda, Maryland, MD 20892, USA.

    https://pubpeer.com/publications/90F12E235052B792EA21E9FE1F2894

  • fernando pessoa October 26, 2017 at 6:40 am

    Br J Cancer. 2000 Sep;83(6):817-25.
    P21-dependent g(1)arrest with downregulation of cyclin D1 and upregulation of cyclin E by the histone deacetylase inhibitor FR901228.
    Sandor V1, Senderowicz A, Mertins S, Sackett D, Sausville E, Blagosklonny MV, Bates SE.
    Author information

    1
    Medicine Branch, DSC, NCI, NIH, Bethesda, MD 20892, USA.

    https://pubpeer.com/publications/1D56B71DA8B291F754A7AA9DAA7CFD

  • fernando pessoa October 26, 2017 at 6:41 am

    Oncogene. 2005 Jul 14;24(30):4829-38.
    Accumulation of hypoxia-inducible factor-1alpha is limited by transcription-dependent depletion.
    Demidenko ZN1, Rapisarda A, Garayoa M, Giannakakou P, Melillo G, Blagosklonny MV.
    Author information

    1
    Brander Cancer Research Institute, New York Medical College, Valhalla, NY, USA.

    https://pubpeer.com/publications/51AD08FE5A2406978057260DA3D02A

  • fernando pessoa October 26, 2017 at 6:42 am

    Carcinogenesis. 2001 Jun;22(6):861-7.
    Inhibition of HIF-1- and wild-type p53-stimulated transcription by codon Arg175 p53 mutants with selective loss of functions.
    Blagosklonny MV1, Giannakakou P, Romanova LY, Ryan KM, Vousden KH, Fojo T.
    Author information

    1
    Medicine Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA.

    457116E5B646B971CE7E4B57DBD9CC

  • fernando pessoa October 26, 2017 at 6:43 am

    Aging (Albany NY). 2013 Jun;5(6):474-84.
    Rapamycin suppresses brain aging in senescence-accelerated OXYS rats.
    Kolosova NG1, Vitovtov AO, Muraleva NA, Akulov AE, Stefanova NA, Blagosklonny MV.
    Author information

    1
    Institute of Cytology and Genetics SB RAS, Acad. , 630090, Novosibirsk, Russia.

    https://pubpeer.com/publications/CC5CE80467519BF525CA1E9D036049

  • fernando pessoa October 26, 2017 at 6:45 am

    Proc Natl Acad Sci U S A. 2012 Aug 14;109(33):13314-8. doi: 10.1073/pnas.1205690109. Epub 2012 Jul 30.
    Hypoxia suppresses conversion from proliferative arrest to cellular senescence.
    Leontieva OV1, Natarajan V, Demidenko ZN, Burdelya LG, Gudkov AV, Blagosklonny MV.
    Author information

    1
    Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA.

    https://pubpeer.com/publications/884A5E8332A265F6B1692B4F487B4B

    • Ana November 1, 2017 at 6:11 am

      Michael Hoffman
      I think it matters less that it’s not indexed in MEDLINE and more that when someone’s grant application or tenure case shows up and has Oncotarget publications those might be dismissed because of the known issues.

      Yes, this is going to be a real issue now.

  • fernando pessoa October 26, 2017 at 6:46 am

    Oncogene. 2007 Oct 18;26(48):6954-8. Epub 2007 May 7.
    p21(Waf1/Cip1/Sdi1) mediates retinoblastoma protein degradation.
    Broude EV1, Swift ME, Vivo C, Chang BD, Davis BM, Kalurupalle S, Blagosklonny MV, Roninson IB.
    Author information

    1
    Cancer Center, Ordway Research Institute, Albany, NY 12208, USA.

    https://pubpeer.com/publications/F2CF584D08DEA944FF6C0E012F236B

  • Paul Brookes October 26, 2017 at 8:22 am

    Does any serious bioscience researcher, academic or otherwise, actually use MedLine to search for literature? I think I used it a couple times back in the days of TelNet, but now everyone just uses PubMed without caring about where the content comes from. We trust NLM/NCBI to curate, and forget about the details of how it works. By continuing to be listed on PubMed, this decision will have virtually no impact on OncoTarget visibility. It’s like a Mom & Pop store ceasing to carry a product, but the product is still freely available on Amazon.

    • Looking Closer October 26, 2017 at 8:59 am

      So, how long before pubmed blacklists journals who continue to publish science fraud? Afterall, publications are the basis of grants.

    • Amanda October 26, 2017 at 9:12 am

      Absolutely they do, considering the number of systematic reviews that intentionally search MedLine rather than PubMed. Many people prefer the advanced search features available through Ovid or other aggregators (which are also available through PubMed, but slightly hidden and not as up front as in Ovid, which forces you to make choices). I’ll agree with your analogy about Amazon, as certainly casual users are often PubMed-exclusive users and I’m not sure enough people pay attention to the distinction. MedLine does seem to be quicker to remove journals when they are bought by known predatory publishers than other databases, such as Embase/CINAHL. See: http://hdl.handle.net/1974/22794

      • Stephen Johnson October 26, 2017 at 1:15 pm

        Amanda, your MEDLINE “rather than PubMed” adds to the confusion of the interface for the content. There is no PubMed search that is not a MEDLINE (+) search unless you use NOT medline[sb] with your search string. The fact that citations from journals that will never be indexed, i.e., never become a MEDLINE record, are in PubMed is really not a problem if one is clear on this distinction. Searching MEDLINE via a non- PubMed interface is probably a bad idea for an SR unless one includes a “pre-MEDLINE” (aka, PubMed records) search. BTW, if you are unable to define “predatory journal,” how can you warn systematic reviewers about them without introducing bias into the SR process? One can more convincingly argue that journal titles and authors should be blinded to reviewers to avoid this kind of publication bias – the quality of the research is what determines if it’s included in final SR analysis, not the relative prestige of the author or journal in which it is published.

    • Michael Hoffman October 26, 2017 at 10:38 am

      I think it matters less that it’s not indexed in MEDLINE and more that when someone’s grant application or tenure case shows up and has Oncotarget publications those might be dismissed because of the known issues.

    • Truth Seeker October 26, 2017 at 1:32 pm

      Paul,

      You are right. Nobody uses meddling anymore. Last time I used it was 17 years ago during my PhD days. As long papers from Oncotarget keep appearing on Pubmed who cares about Medline.

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