Export issues from Embase (Ovid)

plabelle
When using the Chrome extension to export references from Embase (Ovid) to Zotero (Windows Standalone), there are issues with the references when they appear in Zotero. For instance, the authors names are reverse (first name initial appears as last name and last name appears as first name). Then, for articles, the volume, issue and page numbers are all missing. Is there a way to look into these issues? Otherwise, the title, abstract, journal name, year and doi are all properly exported.
  • adamsmith
    I don't have access, so it's a bit tricky -- we're trying to import a format described by OVID as OVID Tagged -- could you see if there's an export option that seems like it corresponds to that (it may be labelled Endnote, but may be something more generic). If so, could you export one problematic item, open with a text editor, and copy & paste here?
  • plabelle
    Here is one example (saved as EndNote format from the Ovid export options).

    <2. >
    VN - Ovid Technologies
    DB - Embase
    UI - 607059520
    EU - 2015552884
    PM - 26522738 [http://www.ncbi.nlm.nih.gov/pubmed/?term=26522738]
    ST - EMBASE
    AU - Sriram C.S.
    AU - Jangra A.
    AU - Gurjar S.S.
    AU - Mohan P.
    AU - Bezbaruah B.K.
    AE - Bezbaruah B.K.; bez_bikki@yahoo.co.in
    IN - (Sriram, Jangra, Bezbaruah) Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Guwahati, Assam 781032, India
    (Gurjar) Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Guwahati, Assam 781032, India
    (Bezbaruah) Department of Pharmacology, Gauhati Medical College, Guwahati, Assam 781032, India
    (Mohan) Department of Pharmacology and Toxicology, College of Veterinary Science, Assam Agricultural University, Khanapara, Guwahati, Assam 781022, India
    AD - B.K. Bezbaruah, Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Narkachal Hilltop, Bhangagarh, Guwahati, Assam 781032, India
    CP - United States
    TI - Edaravone abrogates LPS-induced behavioral anomalies, neuroinflammation and PARP-1.
    SO - Physiology and Behavior. 154 (pp 135-144), 2016. Date of Publication: February 01, 2016.
    PB - Elsevier Inc. (E-mail: usjcs@elsevier.com)
    TJ - Physiology and Behavior
    KW - Anxiety
    KW - Depressive-like behavior
    KW - Edaravone
    KW - Lipopolysaccharide
    KW - Poly(ADP-ribose) polymerase-1
    UR - http://www.elsevier.com/locate/physbeh
    MH - anhedonia
    MH - animal experiment
    MH - animal model
    MH - animal tissue
    MH - antidepressant activity
    MH - antiinflammatory activity
    MH - antioxidant activity
    MH - *anxiety disorder/dt [Drug Therapy]
    MH - anxiety disorder/dt [Drug Therapy]
    MH - article
    MH - behavior assessment
    MH - behavior change
    MH - biochemical analysis
    MH - controlled study
    MH - corticosterone blood level
    MH - cytokine release
    MH - *depression/dt [Drug Therapy]
    MH - depression/dt [Drug Therapy]
    MH - dose response
    MH - drug effect
    MH - drug mechanism
    MH - elevated plus maze test
    MH - enzyme linked immunosorbent assay
    MH - exploratory behavior
    MH - forced swim test
    MH - hippocampus
    MH - light dark test
    MH - lipid peroxidation
    MH - male
    MH - mouse
    MH - *nervous system inflammation/dt [Drug Therapy]
    MH - nervous system inflammation/dt [Drug Therapy]
    MH - nitrosative stress
    MH - nonhuman
    MH - open field test
    MH - oxidative stress
    MH - priority journal
    MH - protein expression
    MH - sucrose preference test
    MH - tail suspension test
    MH - tranquilizing activity
    MH - Western blotting
    MH - brain derived neurotrophic factor/ec [Endogenous Compound]
    MH - catalase/ec [Endogenous Compound]
    MH - corticosterone/ec [Endogenous Compound]
    MH - Escherichia coli lipopolysaccharide
    MH - glutathione/ec [Endogenous Compound]
    MH - interleukin 1beta/ec [Endogenous Compound]
    MH - malonaldehyde/ec [Endogenous Compound]
    MH - nicotinamide adenine dinucleotide/ec [Endogenous Compound]
    MH - *nicotinamide adenine dinucleotide adenosine diphosphate ribosyltransferase 1/ec [Endogenous Compound]
    MH - nitrite/ec [Endogenous Compound]
    MH - *norphenazone/do [Drug Dose]
    MH - *norphenazone/dt [Drug Therapy]
    MH - *norphenazone/ip [Intraperitoneal Drug Administration]
    MH - *norphenazone/pd [Pharmacology]
    MH - superoxide dismutase/ec [Endogenous Compound]
    MH - tumor necrosis factor alpha/ec [Endogenous Compound]
    MH - anxiety
    MH - gene expression
    MH - gene expression regulation
    MH - gene inactivation
    MH - gene overexpression
    MH - *nervous system inflammation
    MH - Swiss Webster mouse
    MH - brain derived neurotrophic factor
    MH - cytokine
    MH - *lipopolysaccharide
    MH - *nicotinamide adenine dinucleotide adenosine diphosphate ribosyltransferase 1
    MH - *norphenazone
    MH - scavenger
    XT - anxiety disorder / drug therapy / norphenazone
    XT - depression / drug therapy / norphenazone
    XT - nervous system inflammation / drug therapy / norphenazone
    XT - norphenazone / drug therapy / anxiety disorder
    XT - norphenazone / drug therapy / depression
    XT - norphenazone / drug therapy / nervous system inflammation
    AB - Poly(ADP-ribose) polymerase-1 (PARP-1) is a DNA nick-sensor enzyme that functions at the center of cellular stress response and affects the immune system at several key points, and thus modulates inflammatory diseases. Our previous study demonstrated that lipopolysaccharide (LPS)-induced depressive-like behavior in mice can be ameliorated by 3-aminobenzamide, which is a PARP-1 inhibitor. In the present study we've examined the effect of a free radical scavenger, edaravone pretreatment against LPS-induced anxiety and depressive-like behavior as well as various hippocampal biochemical parameters including PARP-1. Male Swiss albino mice were treated with edaravone (3 & 10. mg/kg. i.p.) once daily for 14. days. On the 14th day 30. min after edaravone treatment mice were challenged with LPS (1. mg/kg. i.p.). After 3. h and 24. h of LPS administration we've tested mice for anxiety and depressive-like behaviors respectively. Western blotting analysis of PARP-1 in hippocampus was carried out after 12. h of LPS administration. Moreover, after 24. h of LPS administration serum corticosterone, hippocampal BDNF, oxido-nitrosative stress and pro-inflammatory cytokines were estimated by ELISA. Results showed that pretreatment of edaravone (10. mg/kg) ameliorates LPS-induced anxiety and depressive-like behavior. Western blotting analysis showed that LPS-induced anomalous expression of PARP-1 significantly reverses by the pretreatment of edaravone (10. mg/kg).Biochemical analyses revealed that LPS significantly diminishes BDNF, increases pro-inflammatory cytokines and oxido-nitrosative stress in the hippocampus. However, pretreatment with edaravone (10. mg/kg) prominently reversed all these biochemical alterations. Our study emphasized that edaravone pretreatment prevents LPS-induced anxiety and depressive-like behavior, mainly by impeding the inflammation, oxido-nitrosative stress and PARP-1 overexpression. Copyright © 2015.
    RF - 80
    EC - Clinical and Experimental Pharmacology [30], Psychiatry [32], Drug Literature Index [37], General Pathology and Pathological Anatomy [5], Neurology and Neurosurgery [8]
    TN - Sigma Aldrich [United States]
    RN - 218441-99-7 (brain derived neurotrophic factor); 9001-05-2 (catalase); 50-22-6 (corticosterone); 70-18-8 (glutathione); 542-78-9 (malonaldehyde); 53-84-9 (nicotinamide adenine dinucleotide); 14797-65-0 (nitrite); 89-25-8 (norphenazone); 37294-21-6 (superoxide dismutase); 9016-01-7 (superoxide dismutase); 9054-89-1 (superoxide dismutase)
    EZ - EC 1.11.1.6 (catalase); EC 1.15.1.1 (superoxide dismutase).
    IS - 0031-9384
    EN - 1873-507X
    DO - http://dx.doi.org/10.1016/j.physbeh.2015.10.029
    CD - PHBHA
    LG - English
    SL - English
    PT - Journal: Article
    EM - 201641
    DD - 20151224
    DC - 20151209
    YR - 2016
    CR - Copyright 2015 Elsevier B.V., All rights reserved.
    XL - http://ovidsp.ovid.com/ovidweb.cgi?T=JS&CSC=Y&NEWS=N&PAGE=fulltext&D=emedx&AN=607059520
  • plabelle
    Here is another example where there actually is a journal issue number:

    <6. >
    VN - Ovid Technologies
    DB - Embase
    UI - 612339389
    EU - 20160699340
    ST - EMBASE
    AU - Smyth R.M.D.
    AU - Taylor W.
    AU - Heazell A.E.
    AU - Furber C.
    AU - Whitworth M.
    AU - Lavender T.
    AE - Smyth R.M.D.; rebecca.smyth@manchester.ac.uk
    IN - (Smyth, Furber, Lavender) University of Manchester, Division of Nursing Midwifery and Social Work, Manchester M13 9PL, United Kingdom
    (Taylor, Heazell, Whitworth) Maternal and Fetal Health Research Centre 5th Floor (Research), St Mary's Hospital Central Manchester NHS Foundation Trust, St Mary's Hospital, Manchester M13 9WL, United Kingdom
    AD - R.M.D. Smyth, University of Manchester, Division of Nursing Midwifery and Social Work, Manchester M13 9PL, United Kingdom. E-mail: rebecca.smyth@manchester.ac.uk
    CP - United Kingdom
    TI - Women's and clinicians perspectives of presentation with reduced fetal movements: A qualitative study.
    SO - BMC Pregnancy and Childbirth. 16 (1) (no pagination), 2016. Article Number: 280. Date of Publication: 26 Sep 2016.
    PB - BioMed Central Ltd. (E-mail: info@biomedcentral.com)
    TJ - BMC Pregnancy and Childbirth
    KW - Clinicians
    KW - Interviews
    KW - Management
    KW - Maternal experience
    KW - Qualitative
    KW - Reduced fetal movements
    UR - http://www.biomedcentral.com/bmcpregnancychildbirth/
    MH - adverse outcome
    MH - anxiety
    MH - clinical article
    MH - data analysis
    MH - doctor patient relation
    MH - family
    MH - female
    MH - *fetus movement
    MH - human
    MH - maternal care
    MH - pregnancy
    MH - pregnant woman
    MH - *qualitative research
    MH - *semi structured interview
    MH - social network
    AB - Background: Worldwide maternal perception of fetal movements has been used for many years to evaluate fetal wellbeing. It is intuitively regarded as an expression of fetal well-being as pregnancies in which women consistently report regular fetal movements have very low morbidity and mortality. Conversely, maternal perception of reduced fetal movements is associated with adverse pregnancy outcomes. We sought to gain insight into pregnant women's and clinicians views and experiences of reduced movements. Method: We performed qualitative semi-structured interviews with pregnant women who experienced reduced fetal movements in their current pregnancy and health professionals who provide maternity care. Our aim was to develop a better understanding of events, facilitators and barriers to presentation with reduced fetal movements. Data analysis was conducted using framework analysis principles. Results: Twenty-one women and 10 clinicians were interviewed. The themes that emerged following the final coding were influences of social network, facilitators and barriers to presentation and the desire for normality. Conclusions: This study aids understanding about why women present with reduced movements and how they reach the decision to attend hospital. This should inform professionals' views and practice, such that appreciating and addressing women's concerns may reduce anxiety and make presentation with further reduced movements more likely, which is desirable as this group is at increased risk of adverse outcome. To address problems with information about normal and abnormal fetal movements, high-quality information is needed that is accessible to women and their families. Copyright © 2016 The Author(s).
    RF - 32
    EN - 1471-2393
    DO - http://dx.doi.org/10.1186/s12884-016-1074-x
    CD - BPCMB
    LG - English
    SL - English
    PT - Journal: Article
    EM - 201641
    DD - 20161004
    DC - 20161004
    YR - 2016
    CR - Copyright 2016 Elsevier B.V., All rights reserved.
    XL - http://ovidsp.ovid.com/ovidweb.cgi?T=JS&CSC=Y&NEWS=N&PAGE=fulltext&D=emedx&AN=612339389
  • adamsmith
    Great, I should be able to work with that. Will let you know.
    As you can probably imagine, getting the page, volume and issue information from the way it's displayed in a citation (which isn't always formatted the same way) is very tricky (they each should have their own tag), so not sure how much we can do, but I'll certainly try.
    It's really a shame that OVID doesn't invest more in better metadata.
    Those articles are in PubMed with public domain, super-high-quality metadata, so it's really hard to understand.
  • plabelle
    Just wondering if any progress has been made regarding this issue? Thanks.
  • DWL-SDCA
    ...really a shame that OVID doesn't invest...
    It was a few years ago that I talked with an OVID representative on behalf of a student and later in another context (I had to conversationally convince someone there that I wasn't capturing their metadata for use in SafetyLit after written correspondence didn't make sense) about their inconsistent, incoherent, often incorrect, and strange formatting of metadata. The OVID representative made it clear that their garbled metadata was intentional. It is to prevent students from "willy willy nilly nilly" capturing their protected catalog to "make a gigantically massive" collection in violation of "perfectly, reasonably, proper" contract terms with the university.

    I was so impressed with the rep's hyperbolic prose that I took note and sometimes use his words when needed for snark.

    So it isn't that OVID doesn't invest to improve metadata, the opposite (investing effort to manipulate their metadata) appears to be the case.

    Web of Science, Knowledge, etc. does something similar but with articles' titles. It adds hyphens and dashes where there are none and removing such when punctuation exists, interchanging articles (a, the), and performing other tricks. All this in an effort to protect their prouduct by inserting relatively benign Mountweazel copyright traps.



  • plabelle
    Just tested EMBASE again and errors reported in October still occur. Thanks to anyone who might be able to look into this.
  • plabelle
    I know that you might all have been quite busy with Zotero 5.0, but the issues with Zotero and EMBASE (Ovid) remain and are quite annoying. There really doesn't seem to be a workaround through any of the Ovid export options that resolve this issue.
  • DWL-SDCA
    This isn't so much an issue with Zotero as it is with Ovid's practice of providing metadata in non-standard formats. If Ovid provided metadata in a consistently non-standard format, then Zotero translators could allow for that and make improvements. Not only does Ovid not follow standards; the placement of volume, issue, pagination metadata is not consistent from item to item. If it was consistent, even non-standard metadata formatted information could be adjusted by the Zotero translator to make it a better import.

    No other bibliographic management software can do a better job of importing Ovid metadata.
  • adamsmith
    Well, I promised I'll try and I'll still see what we can do, but yes, don't expect anything of great and consistent quality.
  • DWL-SDCA
    In the meantime, please talk with a sympathetic reference librarian and explain the problem. Show her/him an example of the RIS file. Ask if it is possible for the library to file a formal request or complaint with Ovid. There are other services that the library could use that offer the same databases but that provide useful metadata. The price structure for an Ovid subscription isn't typically better than its competitors.

    If the reference librarian doesn't seem to understand your problem, ask if there is someone on the staff who does trainings on the use of personal bibliography managers such as EndNote, Mendeley, or Zotero. That person _will_ understand and may be able to help get Ovid's attention. I hope that if enough libraries complain Ovid will take action.
  • plabelle
    Thanks for the update. I'm a librarian and will definitely follow-up with our Ovid rep. However, what surprises me is that exporting to EndNote from Ovid EMBASE works, so EndNote seems capable of interpreting the weird metadata.
  • adamsmith
    And Endnote is gettig volume and issue numbers for these? I just don't see how that's feasible. Authors, maybe, but the other info? -- I'm not sure if they're getting a different format?

    The last time we tested EndNote on Ovid data it was actually quite bad. I don't have access anymore, so hard for me to tell anymore.
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