retractions in bibtex entries,
Mike Marchywka
marchywka at hotmail.com
Sun Dec 11 00:31:43 CET 2022
On Sat, Dec 10, 2022 at 09:14:05PM +0000, Schneider, Thomas (NIH/NCI) [E] wrote:
> Mike:
>
> > I get pubmed search updates and sometimes there is a retraction
> > notice included. Updates like this can be a problem.
> > This paper was recently retracted,
> >
> > https://pubmed.ncbi.nlm.nih.gov/35815265/
>
> I use my own tcsh script to convert PubMed entries into bibtex format.
> It uses a Pascal program - ancient but reliable tools (like LaTeX!).
>
> https://alum.mit.edu/www/toms/delila/medlinebib.html
>
> So I ran it. I got this entry:
>
> @article{Zhang.Wang2022,
> author = "H. Zhang
> and J. Xian
> and Y. Li
> and L. Xiao
> and L. Wang",
> title = "{Effects of Tenofovir Combined with Recombinant Human
> Interferon alpha-2b on Negative Conversion Rate, Liver Function,
> Immune Status, and Drug Safety in Patients with Chronic Hepatitis B:
> A Systematic Review and Meta-Analysis}",
> journal = "Evid Based Complement Alternat Med",
> volume = "2022",
> pages = "1889628",
> pmid = "35815265",
> pmcid = "PMC9262527",
> note = "\url
> {https://doi.org/10.1155/2022/1889628}",
> comment = "2022/12/10 16:00:11 ",
> year = "2022"}
>
> While generating that it told me that the way to get the medline
> format entry is:
>
> https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=35815265&rettype=medline&retmode=text
See below, but
IIRC, my script does it in two requests with this being the fetch,
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?tool=biotechmarchywka&email=marchywka@hotmail.com&rettype=medline&retmode=text&retstart=0&retmax=1&db=pubmed&query_key=1&WebEnv=MCID_63951073a293d76eb91c7f17
>
Thanks. Actually this is what I should try first but I checked the
file and wget could not find the server ?!?!?!?. I have noticed
several times lately that the pubmed links seem to be slow
and go to the fetchpage handlers instead of using eutils but I
don't usually check. WTH it would have DNS problems is beyond me-
in the past the PMCID was not found on very recent articles
so I assumed it may just be flakey at the NCBI.
But, this last run worked and one design feature was to include
unused fields like "PT" as a comment and this what happened here,
toobib -clip
mjm>clip xxxx
./toobib.h546 cmd=clip p1=xxxx p2= flags=18 x.flag_to_string(flags,0)=show_trial paste_citation
./mjm_med2bib_guesses.h990 uin=https://pubmed.ncbi.nlm.nih.gov/35815265/ dest=xxxx flags=18
./mjm_med2bib_guesses.h1164 % mjmhandler: toobib guesspubmed
% date 2022-12-10:18:04:21 Sat Dec 10 18:04:21 EST 2022
% srcurl: https://pubmed.ncbi.nlm.nih.gov/35815265/
% citeurl: eutilsnew -out "/tmp/filenqXJMf.outguesses" -v -db pubmed -report medline 35815265
%CI = {Copyright (c) 2022 Hui Zhang et al.},
%COIS = {The authors declare that they have no conflicts of interest.},
%CRDT = {2022/07/11 04:30},
%DP = {2022},
%EDAT = {2022/07/12 06:00},
%JID = {101215021},
%LA = {eng},
%LR = {20221209},
%MHDA = {2022/07/12 06:01},
%OWN = {NLM},
%PL = {United States},
%PST = {epublish},
%PT = {Retracted Publication},
%RIN = {Evid Based Complement Alternat Med. 2022 Nov 29;2022:9791408. PMID: 36482933},
%SO = {Evid Based Complement Alternat Med. 2022 Jun 30;2022:1889628. doi: 10.1155/2022/1889628. eCollection 2022.},
%STAT = {PubMed-not-MEDLINE},
%TA = {Evid Based Complement Alternat Med}
@article{PMC9262527,
X_TooBib = {date: 20220630},
X_TooBib = {urldate: FixBeKvp s= cmd=date "+%Y-%m-%d" d=2022-12-10 dn=urldate},
X_TooBib = {publisher: ReWriteParse be.get(s)= be.get(dest)=},
X_TooBib = {author: Zhang , Hui and Xian , Jianchun and Li , Yang and Xiao , Li and Wang , Lu},
abstract = {OBJECTIVE: To systematically evaluate the clinical value of tenofovir combined with recombinant human interferon alpha-2b in the treatment of chronic hepatitis B and to provide evidence-based medicine for its popularization and use. METHODS: The randomized controlled trials (RCTs) of tenofovir combined with recombinant human interferon alpha-2b in the online database of PubMed, EMBASE, ScienceDirect, Cochrane Library, China knowledge Network (CNKI), China VIP database, Wanfang database, and China Biomedical Literature Database (CBM) were searched. The data included in this study were extracted by two independent researchers. After extracting the data of the study, the Cochrane manual 5.1.0 standard was used to evaluate the bias risk of all the literature included in this study. RevMan5.4 statistical software was used to analyze the collected data by meta. RESULTS: Entecavir combined with recombinant human interferon alpha-2b can inhibit the activity of HBV polymerase and improve the inflammatory response of the liver. Recombinant human interferon alpha-2b can regulate immune function by inducing T cell differentiation and maturation and enhancing the production of cytokines. The systematic evaluation showed that entecavir combined with recombinant human interferon alpha-2b had higher serum HBeAg negative conversion rate, higher drug safety compared with entecavir alone, and improved liver function and immune status. CONCLUSION: Tenofovir combined with recombinant human interferon alpha-2b has a high serum HBeAg negative rate and safety profile for the treatment of chronic hepatitis B. The combination treatment can improve liver function and immune status in patients, but more studies with higher methodological quality and longer duration of intervention are needed for further validation.},
address = {The Medical Department of Neurology, Jiangsu Taizhou People's Hospital, Taizhou 225300, China.},
auid = {ORCID: 0000-0002-1266-7916},
author = {Zhang , Hui and Xian , Jianchun and Li , Yang and Xiao , Li and Wang , Lu},
author_orig = {Zhang, Hui and Xian, Jianchun and Li, Yang and Xiao, Li and Wang, Lu},
date = {20220630},
date_orig = {20220630 },
day = {30},
doi = {10.1155/2022/1889628},
issue = {1741-427X (Linking)},
journal = {Evidence-based complementary and alternative medicine : eCAM},
month = {06},
pages = {1889628},
phst = {2022/05/07 00:00 [received] , 2022/05/25 00:00 [revised] , 2022/05/29 00:00 [accepted] , 2022/07/11 04:30 [entrez] , 2022/07/12 06:00 [pubmed] , 2022/07/12 06:01 [medline]},
title = {Effects of Tenofovir Combined with Recombinant Human Interferon alpha-2b on Negative Conversion Rate, Liver Function, Immune Status, and Drug Safety in Patients with Chronic Hepatitis B: A Systematic Review and Meta-Analysis.},
urldate = {2022-12-10},
voiume = {2022},
year = {2022},
final_assembly ={ TooBib handler guesspubmed},
url={https://pubmed.ncbi.nlm.nih.gov/35815265/},
srcurl={https://pubmed.ncbi.nlm.nih.gov/35815265/},
xsrcurl={https://pubmed.ncbi.nlm.nih.gov/35815265/},
citeurl={eutilsnew},
toobib-date={2022-12-10:18:04:21 Sat Dec 10 18:04:21 EST 2022}
}
./mjm_med2bib_guesses.h1172 saving to df=xxxx
./mjm_med2bib_guesses.h1186 have citation nfound=1 cite=\cite{PMC9262527} something=1 paste_citation=1
mjm>
I modified the code to deal with the "PT" field however.
Now it includes it in the bibtex although the phst field should have
a date retract entry :) ,
phst = {2022/05/07 00:00 [received] , 2022/05/25 00:00 [revised] , 2022/05/29 00:00 [accepted] , 2022/07/11 04:30 [entrez] , 2022/07/12 06:00 [pubmed] , 2022/07/12 06:01 [medline]},
pubtype = {Retracted Publication},
title = {Effects of Tenofovir Combined with Recombinant Human Interferon alpha-2b on Negative Conversion Rate, Liver Function, Immune Status, and Drug Safety in Patients with Chronic Hepatitis B: A Systematic Review and Meta-Analysis.},
urldate = {2022-12-10},
> If you try this link, it should be a clean text page (attached).
>
You link worked right away, no idea why mine are having DNS and https
errors to their server. I am using lynx or wget.
> My medlinebib program parses this since it is a reliable format.
>
> In there I found:
>
> PT - Retracted Publication
>
> So you can use that to identify retracted publications - no unreliable
> html scraping needed!!
>
> Tom
>
> Thomas D. Schneider, Ph.D.
> Senior Investigator
> National Institutes of Health
> National Cancer Institute
> Center for Cancer Research
> RNA Biology Laboratory
> Biological Information Theory Group
> Frederick, Maryland 21702-1201
> schneidt at mail.nih.gov
> alum.mit.edu/www/toms
> https://alum.mit.edu/www/toms
>
>
> PMID- 35815265
> OWN - NLM
> STAT- PubMed-not-MEDLINE
> LR - 20221209
> IS - 1741-427X (Print)
> IS - 1741-4288 (Electronic)
> IS - 1741-427X (Linking)
> VI - 2022
> DP - 2022
> TI - Effects of Tenofovir Combined with Recombinant Human Interferon alpha-2b on Negative
> Conversion Rate, Liver Function, Immune Status, and Drug Safety in Patients with
> Chronic Hepatitis B: A Systematic Review and Meta-Analysis.
> PG - 1889628
> LID - 10.1155/2022/1889628 [doi]
> LID - 1889628
> AB - OBJECTIVE: To systematically evaluate the clinical value of tenofovir combined
> with recombinant human interferon alpha-2b in the treatment of chronic hepatitis B
> and to provide evidence-based medicine for its popularization and use. METHODS:
> The randomized controlled trials (RCTs) of tenofovir combined with recombinant
> human interferon alpha-2b in the online database of PubMed, EMBASE, ScienceDirect,
> Cochrane Library, China knowledge Network (CNKI), China VIP database, Wanfang
> database, and China Biomedical Literature Database (CBM) were searched. The data
> included in this study were extracted by two independent researchers. After
> extracting the data of the study, the Cochrane manual 5.1.0 standard was used to
> evaluate the bias risk of all the literature included in this study. RevMan5.4
> statistical software was used to analyze the collected data by meta. RESULTS:
> Entecavir combined with recombinant human interferon alpha-2b can inhibit the
> activity of HBV polymerase and improve the inflammatory response of the liver.
> Recombinant human interferon alpha-2b can regulate immune function by inducing T cell
> differentiation and maturation and enhancing the production of cytokines. The
> systematic evaluation showed that entecavir combined with recombinant human
> interferon alpha-2b had higher serum HBeAg negative conversion rate, higher drug
> safety compared with entecavir alone, and improved liver function and immune
> status. CONCLUSION: Tenofovir combined with recombinant human interferon alpha-2b
> has a high serum HBeAg negative rate and safety profile for the treatment of
> chronic hepatitis B. The combination treatment can improve liver function and
> immune status in patients, but more studies with higher methodological quality
> and longer duration of intervention are needed for further validation.
> CI - Copyright (c) 2022 Hui Zhang et al.
> FAU - Zhang, Hui
> AU - Zhang H
> AD - The Medical Department of Hepatology, Jiangsu Taizhou People's Hospital, Taizhou
> 225300, China.
> FAU - Xian, Jianchun
> AU - Xian J
> AD - The Medical Department of Hepatology, Jiangsu Taizhou People's Hospital, Taizhou
> 225300, China.
> FAU - Li, Yang
> AU - Li Y
> AD - The Medical Department of Hepatology, Jiangsu Taizhou People's Hospital, Taizhou
> 225300, China.
> FAU - Xiao, Li
> AU - Xiao L
> AD - The Medical Department of Hepatology, Jiangsu Taizhou People's Hospital, Taizhou
> 225300, China.
> FAU - Wang, Lu
> AU - Wang L
> AUID- ORCID: 0000-0002-1266-7916
> AD - The Medical Department of Neurology, Jiangsu Taizhou People's Hospital, Taizhou
> 225300, China.
> LA - eng
> PT - Journal Article
> PT - Retracted Publication
> DEP - 20220630
> PL - United States
> TA - Evid Based Complement Alternat Med
> JT - Evidence-based complementary and alternative medicine : eCAM
> JID - 101215021
> RIN - Evid Based Complement Alternat Med. 2022 Nov 29;2022:9791408. PMID: 36482933
> PMC - PMC9262527
> COIS- The authors declare that they have no conflicts of interest.
> EDAT- 2022/07/12 06:00
> MHDA- 2022/07/12 06:01
> CRDT- 2022/07/11 04:30
> PHST- 2022/05/07 00:00 [received]
> PHST- 2022/05/25 00:00 [revised]
> PHST- 2022/05/29 00:00 [accepted]
> PHST- 2022/07/11 04:30 [entrez]
> PHST- 2022/07/12 06:00 [pubmed]
> PHST- 2022/07/12 06:01 [medline]
> AID - 10.1155/2022/1889628 [doi]
> PST - epublish
> SO - Evid Based Complement Alternat Med. 2022 Jun 30;2022:1889628. doi:
> 10.1155/2022/1889628. eCollection 2022.
--
mike marchywka
306 charles cox
canton GA 30115
USA, Earth
marchywka at hotmail.com
404-788-1216
ORCID: 0000-0001-9237-455X
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