another website making bibtex download difficult,
Mike Marchywka
marchywka at hotmail.com
Mon Oct 16 13:58:49 CEST 2023
On Mon, Oct 16, 2023 at 11:10:12AM +0000, Schneider, Thomas (NIH/NCI) [E] wrote:
> Mike:
>
> For me the The url was mangled by the idiotic 'safelinks'. Undoing
> that gave:
>
> https://www.jbc.org/article/S0021-9258
>
Thanks for your interest. The link in the copy I received
from the mail list works for me, you may be able to
"view message source" to see what was actually sent.
As you note later, the parens may be confusing this is the
link w/o protocol,
www.jbc.org/article/S0021-9258(19)72469-7/fulltext
> which fails:
>
> > An error has occurred
> >
> > The page or action you requested has resulted in an error. Please go
> > back to the previous page by using your browser's Back button, or
> > visit the Home Page.
> >
> > This page does not exist
>
> I then put 'S0021-9258' into the search on that page and got
>
> https://www.jbc.org/action/doSearch?type=quicksearch&text1=S0021-9258&field1=AllField
>
> Guessing that the first paper is what you want gave:
>
> https://www.jbc.org/article/S0021-9258(18)41411-1/fulltext
>
> So the first thing is that JBC used unusual '(' and ')' in the url which
> is probably a very bad idea. Whatever tools you use (or the safelinks)
> may have broken the URL at the parens.
>
> The paper title is:
>
> A naturally occurring point mutation confers broad range tolerance to
> herbicides that target acetolactate synthase.
>
Did my Toobib bibtex entry show up? The point of course is to
document the citation for this purpose among others :)
Some of the bibtex entries that may help include the following
excerpts. Note that have a cleaner "resource" url
that may be friendlier,
abbrvjrnl = {Journal of Biological Chemistry},
alternative-id = {S0021925819724697},
author = {Chyan , Yau-Jan and Poeggeler , Burkhard and Omar , Rawhi A. and Chain , Daniel G. and Frangione , Blas and Ghiso , Jorge and Pappolla , Miguel A.},
author_orig = {Yau-Jan Chyan and Burkhard Poeggeler and Rawhi A. Omar and Daniel G. Chain and Blas Frangione and Jorge Ghiso and Miguel A. Pappolla},
bib-source = {Crossref},
date = {1999},
date-issued = {1999-07},
date-journal-issue = {1999-07},
date-published-print = {1999-07},
date_orig = { 1999-07 1999-07 1999-07 },
deposited = {1641238993000},
doi = {10.1074/jbc.274.31.21937},
issn = {0021-9258},
issn-type = {0021-9258, print},
issue = {31},
journal = {Journal of Biological Chemistry},
journal-issue = {31},
language = {en},
page = {21937-21942},
prefix = {10.1016},
publication-date = {1999-07},
publisher = {Elsevier BV},
resource = {https://linkinghub.elsevier.com/retrieve/pii/S0021925819724697},
title = {Potent Neuroprotective Properties against the Alzheimer upbeta-Amyloid by an Endogenous Melatonin-related Indole Structure, Indole-3-propionic Acid},
title_as_rcvd = {Potent Neuroprotective Properties against the Alzheimer -Amyloid by an Endogenous Melatonin-related Indole Structure, Indole-3-propionic Acid},
url = {http://dx.doi.org/10.1074/jbc.274.31.21937},
volume = {274},
year = {1999},
> giving that to PubMed
>
> https://pubmed.ncbi.nlm.nih.gov/?term=A+naturally+occurring+point+mutation+confers+broad+range+tolerance+to+herbicides+that+target+acetolactate+synthase
>
> gives two hits = same title, different times. The second is an
> Erratum, I will ignore that. The first is a fine entry:
>
> https://pubmed.ncbi.nlm.nih.gov/8690734/
>
Yes pubmed works for a lot of things but when you can't
read the page and there is no doi in the link you can
be stuck unless you know another code in the link.
> I have a tool, medlinebib, that converts that to bibex format:
> https://alum.mit.edu/www/toms/delila/medlinebib.html
> The result is:
>
> @article{Bernasconi.Siehl1996,
> author = "P. Bernasconi
> and A. R. Woodworth
> and B. A. Rosen
> and M. V. Subramanian
> and D. L. Siehl",
> title = "{A naturally occurring point mutation confers broad range
> tolerance to herbicides that target acetolactate synthase}",
> journal = "J Biol Chem",
> volume = "271",
> pages = "13925",
> pmid = "8690734",
> pmcid = "\todobf{MISSING}",
> note = "\url
> {https://doi.org/\todobf{MISSING}}",
> comment = "2023/10/16 07:04:34 ",
> year = "1996"}
>
> Note that there IS a doi on the website
> (https://doi.org/10.1074/jbc.270.29.17381), so on ecould put that into
> the note to get a viable link.
>
With that link toobib's first result is just the doi in the link
and that is very reliable and fast,
toobib -clip
mjm>clip xxxx
./toobib.h588 cmd=clip p1=xxxx p2= flags=18 x.flag_to_string(flags,0)=show_trial paste_citation
./mjm_med2bib_guesses.h997 uin=https://doi.org/10.1074/jbc.270.29.17381 dest=xxxx flags=18
./mjm_med2bib_guesses.h1171 % mjmhandler: toobib guesssdoi(crossref)
% date 2023-10-16:07:57:16 Mon 16 Oct 2023 07:57:16 AM EDT
% srcurl: https://doi.org/10.1074/jbc.270.29.17381
% citeurl: http://api.crossref.org/works/10.1074/jbc.270.29.17381
@article{Bernasconi_Woodworth_Rosen_Naturally_Occurring_Point_1995,
X_TooBib = {date: 1995},
X_TooBib = {year: 1995, infield_fix_dates },
X_TooBib = {urldate: FixBeKvp s= cmd=date "+%Y-%m-%d" d=2023-10-16 dn=urldate},
X_TooBib = {author: Bernasconi , Paul and Woodworth , Alison R. and Rosen , Barbara A. and Subramanian , Mani V. and Siehl , Daniel L.},
abbrvjrnl = {Journal of Biological Chemistry},
affiliation = {},
alternative-id = {S0021925818956243},
author = {Bernasconi , Paul and Woodworth , Alison R. and Rosen , Barbara A. and Subramanian , Mani V. and Siehl , Daniel L.},
author_orig = {Paul Bernasconi and Alison R. Woodworth and Barbara A. Rosen and Mani V. Subramanian and Daniel L. Siehl},
bib-source = {Crossref},
content-domain = {false},
date = {1995},
date-created = {2002-07-26T14:52:50Z},
date-deposited = {2021-12-182021-12-18T09:16:19Z},
date-indexed = {2023-10-16T02:13:43Z},
date-issued = {1995-07},
date-journal-issue = {1995-07},
date-license = {1995-07-011995-07-01T00:00:00Z-2020-11-102020-11-10T00:00:00Z},
date-published-print = {1995-07},
date_orig = { 1995-07 1995-07 1995-07 },
deposited = {1639818979000},
doi = {10.1074/jbc.270.29.17381},
is-referenced-by-count = {191},
issn = {0021-9258},
issn-type = {0021-9258, print},
issue = {29},
journal = {Journal of Biological Chemistry},
journal-issue = {29},
language = {en},
license = {804556800000, tdm, 0, https://www.elsevier.com/tdm/userlicense/1.0/, 1604966400000, vor, 9264, http://creativecommons.org/licenses/by/4.0/},
link = {https://api.elsevier.com/content/article/PII:S0021925818956243?httpAccept=text/xml, text/xml, vor, text-mining, https://api.elsevier.com/content/article/PII:S0021925818956243?httpAccept=text/plain, text/plain, vor, text-mining, https://syndication.highwire.org/content/doi/10.1074/jbc.270.29.17381, unspecified, vor, similarity-checking},
member = {78},
page = {17381-17385},
prefix = {10.1016},
publication-date = {1995-07},
publisher = {Elsevier BV},
reference = {deleted},
reference-count = {28},
references-count = {28},
resource = {https://linkinghub.elsevier.com/retrieve/pii/S0021925818956243},
score = {1},
subject = {Biochemistry},
title = {A Naturally Occurring Point Mutation Confers Broad Range Tolerance to Herbicides That Target Acetolactate Synthase},
type = {journal-article},
url = {http://dx.doi.org/10.1074/jbc.270.29.17381},
urldate = {2023-10-16},
volume = {270},
year = {1995},
final_assembly ={ TooBib handler guesssdoi(crossref)},
srcurl={https://doi.org/10.1074/jbc.270.29.17381},
xsrcurl={https://doi.org/10.1074/jbc.270.29.17381},
citeurl={http://api.crossref.org/works/10.1074/jbc.270.29.17381},
toobib-date={2023-10-16:07:57:16 Mon 16 Oct 2023 07:57:16 AM EDT}
}
./mjm_med2bib_guesses.h1179 saving to df=xxxx
./mjm_med2bib_guesses.h1193 have citation nfound=1 cite=\cite{Bernasconi_Woodworth_Rosen_Naturally_Occurring_Point_1995} something=1 paste_citation=1
mjm>
Thanks.
> 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
>
--
mike marchywka
44 Crosscreek Trail
Jasper GA 30143
USA, Earth marchywka at hotmail.com
404-788-1216 ORCID: 0000-0001-9237-455X
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