putting back on list , sorry, Fw: anyone want to look at this pdf and determine what is going on with the extended info, thanks.

Mike Marchywka marchywka at hotmail.com
Fri Jul 24 14:31:28 CEST 2020

From: Mike Marchywka <marchywka at hotmail.com>
Sent: Friday, July 24, 2020 5:44 AM
To: Schneider, Thomas (NIH/NCI) [E]
Subject: Re: anyone want to look at this pdf and determine what is going on with the  extended info, thanks.

On Fri, Jul 24, 2020 at 08:17:33AM +0000, Schneider, Thomas (NIH/NCI) [E] wrote:
> Mike:
> > Thanks. That looks about right.
> By the way, the script calls a Pascal program of mine.  So you
> will need to compile it (gnu pascal compiler on linux or p2c on
> Mac).
> > Is that all automated or do you need to copy/paste?
> I have a couple tools for getting to the pubmed id.  One is yvp (see
> my tools on my website) or yvpg or yvpgt.  But copy paste of the title
> into pubmed is quite effective these days.  Sometimes I get the PMID
> on my personal computer and type it into my work computer cut/paste
> buffer (see the fb script for editing the cut/paste buffer on a Mac!).
> Then I paste it like this on the command line:
> % cd
> % mq 32680882
> mq is a pointer to medlinequery which makes it trivial to do.

I tried to move all the manual stuff to just fixing a tentative
bibtex download - I've got things like fixing gross errors
from publishers or maybe they use latex for symbols that doesn't
work. However, the logic for the auomtated approaches has gone
through a learning curve and I think now I could make a better
one. Right now, I just copy the link to whatever I want to cite,
this may even work from some local files, and the script
looks for ways it could get the bibtex. So, with uri on clipboard,

med2bib -cite > xxxx

and it puts a bibtex into xxxx and search strategy to stderr.
And then I can rerun omiting some sources to find alts, for example,

med2bib -no citeseer -cite > xxxx
med2bib -no headless -cite > xxxx
med2bib -no jstor -cite > xxxx2
med2bib -no karger -cite > xxxx
med2bib -no mdpi -cite > xxxx
med2bib -no researchgate -cite > xxxx
med2bib -no wiley -cite > xxxx

Although now I guess I would get all that may apply and
finish my bibtex sort/merge too for manual curation.
I try not to modify the downloaded bibtex much at this point
but put in latex "%" comment lines prior to it and then may
merge in c++ tool later.
After manual inspection, I run a validator ( simple latex file )
and add to bibliography ( downloaded xxxx merged into non_pmc_covid19.bib ),

med2bib -exportbib xxxx covid19

I started to replace the med2bib bash script with c++ code to get
nice data sturctures but did not get far and still update this

> In my references directory I have a soft link 'b' that points to the
> ~/bibformat.  I read that into my all.bib and it's done.  All this
> takes a few seconds.  By using tools I can do it any of several ways
> quickly.
> > I usually will use the PMID if I'm on pubmed but otherwise
> > try to get a doi or scrape a bibtex link from a webpage.
> It's super fast if you go through pubmed and get the medline format.

I do that but their new format fools the scripts and it finds the doi...

> I have a script 'pubmed'.  A pointer to it sits on my desktop.  I
> gather stuff (like a title) for a pubmed search into my cut/paste
> buffer and double clickthe icon.  Then I'm "on pubmed" in a few
> seconds.  (Likewise the 'gose' script would do a google search.) (Note
> again, the 'fb' script allows me to edit the cut/paste buffer so I can
> get the search the way I want; it also sits on my desktop.)
> See the script for how to do that.  Then you can convert the medline
> format yourself or use my script/program.
> > I guess one question is what all that "zotero" stuff is as
> > it does not seem to relate to the topic of the paper.
> I don't use zotero.

Neither do I but if the info is there to scrape great. Since it
does not seem to relate curious on any conjecture on how it got
there and if this is likely to be a common error.

> > However, in terms of the immediate issue, getting the bibtex,
> > when I used the doi extraction, I ended up with this. From the
> > firt few lines the script found the first bibtex entry by scraping
> > a doi from the pdf and crossref had a usable result.
> Ok ...


> 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
>   https://alum.mit.edu/www/toms

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