more on retraction bibtex and TooBib upgrade :)

Fri Jun 2 13:26:34 CEST 2023

I got another retration alert on pubmed today
for this article,

https://pubmed.ncbi.nlm.nih.gov/31058405/
https://onlinelibrary.wiley.com/doi/10.1002/adma.201900813

The zotero webform kindly provided by someone on this list,
https://zbib.org/

returned the following with no obvious mention of retraction
although it did flag the possiblity the two links
point to the same work, 

cat  ~/Downloads/citations.bib  

@article{li_phosphorus-rich_2019,
	title = {Phosphorus-{Rich} {Colloidal} {Cobalt} {Diphosphide} ({CoP2} ) {Nanocrystals} for {Electrochemical} and {Photoelectrochemical} {Hydrogen} {Evolution}},
	volume = {31},
	issn = {1521-4095},
	doi = {10.1002/adma.201900813},
	abstract = {Developing earth-abundant and efficient electrocatalysts for photoelectrochemical water splitting is critical to realizing a high-performance solar-to-hydrogen energy conversion process. Herein, phosphorus-rich colloidal cobalt diphosphide nanocrystals (CoP2 NCs) are synthesized via hot injection. The CoP2 NCs show a Pt-like hydrogen evolution reaction (HER) electrocatalytic activity in acidic solution with a small overpotential of 39 mV to achieve -10 mA cm-2 and a very low Tafel slope of 32 mV dec-1 . Density functional theory (DFT) calculations reveal that the high P content both physically separates Co atoms to prevent H from over binding to multiple Co atoms, while simultaneously stabilizing H adsorbed to single Co atoms. The catalytic performance of the CoP2 NCs is further demonstrated in a metal-insulator-semiconductor photoelectrochemical device consisting of bottom p-Si light absorber, atomic layer deposition Al-ZnO passivation layers, and the CoP2 cocatalyst. The p-Si/AZO/TiO2 /CoP2 photocathode shows a photocurrent density of -16.7 mA cm-2 at 0 V versus reversible hydrogen electrode (RHE) and an output photovoltage of 0.54 V. The high performance and stability are attributed to the junction between p-Si and AZO, the corrosion-resistance of the pinhole-free TiO2 protective layer, and the fast HER kinetics of the CoP2 NCs.},
	language = {eng},
	number = {24},
	journal = {Advanced Materials (Deerfield Beach, Fla.)},
	author = {Li, Hui and Wen, Peng and Itanze, Dominique S. and Kim, Michael W. and Adhikari, Shiba and Lu, Chang and Jiang, Lin and Qiu, Yejun and Geyer, Scott M.},
	month = jun,
	year = {2019},
	pmid = {31058405},
	keywords = {cobalt diphosphide, density functional theory, in situ XAS, metal-insulator-semiconductor, photoelectrochemical water splitting},
	pages = {e1900813},
}

@article{li_phosphorusrich_2019,
	title = {Phosphorus‐{Rich} {Colloidal} {Cobalt} {Diphosphide} ({CoP} $_{\textrm{2}}$ ) {Nanocrystals} for {Electrochemical} and {Photoelectrochemical} {Hydrogen} {Evolution}},
	issn = {0935-9648, 1521-4095},
	url = {https://onlinelibrary.wiley.com/doi/10.1002/adma.201900813},
	doi = {10.1002/adma.201900813},
	language = {en},
	urldate = {2023-06-02},
	journal = {Advanced Materials},
	author = {Li, Hui and Wen, Peng and Itanze, Dominique S. and Kim, Michael W. and Adhikari, Shiba and Lu, Chang and Jiang, Lin and Qiu, Yejun and Geyer, Scott M.},
	month = may,
	year = {2019},
	pages = {1900813},
}
marchywka at happy:/home/documents/cpp/proj/toobib$ cat  ~/Downloads/citations.bib   | grep -i retra

I recently upgraded from Ubuntu Beaver to Focal due to an apparent disk
drive failure and found among other things that the later headless chrome
versions may be much improved. I thought some issues were inherent in my
asynchronous logic but maybe not :) Due to the architecture, TooBib 
uses c++ std::system to invoke arbitrary utilities, I had to 
re-install a lot of little things but so far nothing major. 
In any case, it looks like the pubmed retraction is still
as it has been with medline and the liberal scraping mode finding
evidence of retraction but not the other modes. 
The publisher's site is a little better. Below are the retraction
indications TooBib found for various handlers with either link,

pubmed link.
grep -i "retract\|mjmhandle"  pubmed_link1.txt
% mjmhandler: toobib guesspubmed
%PT = {Retracted Publication},
pubtype = {Journal Article Retracted Publication},
% mjmhandler: toobib handledoi(crossref)
% mjmhandler: toobib handledoi(crossref)
% mjmhandler: toobib handledoi(crossref)
% mjmhandler: toobib handledoixml ( quality i=0 szr=7 goods=1 )(crossref)
% mjmhandler: toobib handlepdfstrings(crossref)
% mjmhandler: toobib handleadhochtml<-citation
% mjmhandler: toobib handleadhochtml<-og
% mjmhandler: toobib handleadhochtml<-all
keywords = {pmid:31058405, doi:10.1002/adma.201900813, Retracted Publication, Hui Li, Peng Wen, Scott M Geyer, PubMed Abstract, NIH, NLM, NCBI, National Institutes of Health, National Center for Biotechnology Information, National Library of Medicine, MEDLINE},
% mjmhandler: toobib handlegsmeta(scraper)
% mjmhandler: toobib handlegsmeta(html)
% mjmhandler: toobib handleheadless<-handledoi
% mjmhandler: toobib handleheadless<-handlepdfstrings
marchywka at happy:/home/documents/cpp/proj/toobib$ 

publisher link,

 grep -i "retract\|mjmhandle"  pubmed_link2.txt
% mjmhandler: toobib handledoilink(idiourl,  decodes=0)(crossref)
% mjmhandler: toobib handledoilink(crossref)
% mjmhandler: toobib handledoilink(idiourl,  decodes=0)(crossref)
% mjmhandler: toobib handledoilink(crossref)
% mjmhandler: toobib handledoilink(idiourl,  decodes=0)(crossref)
% mjmhandler: toobib handledoilink(crossref)
% mjmhandler: toobib handledoi(crossref)
% mjmhandler: toobib handledoi(crossref)
% mjmhandler: toobib handledoixml ( quality i=0 szr=2 goods=1 )(crossref)
% mjmhandler: toobib handlepdfstrings(crossref)
% mjmhandler: toobib handleadhochtml<-citation
@article{Li_Wen_Itanze_Retracted_Phosphorus_Rich_Colloidal_2019,
title = {Retracted: Phosphorus-Rich Colloidal Cobalt Diphosphide (CoP2) Nanocrystals for Electrochemical and Photoelectrochemical Hydrogen Evolution},
% mjmhandler: toobib handleadhochtml<-og
@article{DUM_Retracted_PhosphorusRich_Colloidal_Cobalt_,
title = {Retracted: PhosphorusRich Colloidal Cobalt Diphosphide (CoP2) Nanocrystals for Electrochemical and Photoelectrochemical Hydrogen Evolution},
% mjmhandler: toobib handleadhochtml<-all
citation_title = {Retracted: Phosphorus-Rich Colloidal Cobalt Diphosphide (CoP2) Nanocrystals for Electrochemical and Photoelectrochemical Hydrogen Evolution},
og:title = {Retracted: PhosphorusRich Colloidal Cobalt Diphosphide (CoP2) Nanocrystals for Electrochemical and Photoelectrochemical Hydrogen Evolution},
% mjmhandler: toobib handlegsmeta(scraper)
@article{Retracted_Phosphorus_Rich_Colloidal_Peng_2019,
title = {Retracted: Phosphorus-Rich Colloidal Cobalt Diphosphide (CoP2) Nanocrystals for Electrochemical and Photoelectrochemical Hydrogen Evolution},

IIRC Zotero prefers to scrape html over the DOI entry so I'm surprised
it did not find this in the second link. 
Also TooBib "-all" mode only find a few directly available
ways to get a bibex entry but does not crawl. Notably it did not
find the publisher link via the doi on the pubmed entry page.
I guess now that headless chrome seems to work much faster I can 
have an extended crawl mode to find even more bibtex :)

fwiw.

Bibtex entries still seem to be a hunter-gatherer art rather than
a science lol.

-- 

mike marchywka
44 Crosscreek Trail
Jasper GA 30143
USA, Earth marchywka at hotmail.com
 404-788-1216 ORCID: 0000-0001-9237-455X