When importing citations from PubMed some of the longer abstracts are truncated. Is there a way to change this to enable the entire abstract to be imported?
Know that Oxford University Press journal articles' abstracts (in their metadata) are 'pre-truncated' by the publisher at a specified number of characters.
I saved this txt pubmed file: ( I have inserted several lines of space at the point where the abstract gets cut off.)
PMID- 31642559 OWN - NLM STAT- MEDLINE DCOM- 20200225 LR - 20200421 IS - 1365-2184 (Electronic) IS - 0960-7722 (Print) IS - 0960-7722 (Linking) VI - 53 IP - 1 DP - 2020 Jan TI - Withaferin A triggers G2/M arrest and intrinsic apoptosis in glioblastoma cells via ATF4-ATF3-CHOP axis. PG - e12706 LID - 10.1111/cpr.12706 [doi] LID - e12706 AB - OBJECTIVE: Withaferin A (WA) is a bioactive compound with a remarkable anti-cancer effect derived from Withania somnifera, commonly known as ashwagandha. However, the anti-cancer mechanisms of WA in glioblastoma multiforme (GBM) are still unclear. MATERIALS AND METHODS: Cell viability assays and xenografted nude mice were used to evaluate the effects of WA, along with flow cytometry to detect apoptosis and cell cycle of GBM. RNA-seq analysis, Western blotting, immunofluorescence staining, qRT-PCR and siRNA gene silencing were carried out to determine the signalling pathways affected by WA. RESULTS: Withaferin A significantly inhibited the growth of GBM in vitro and in vivo and triggered the intrinsic apoptosis of GBM cells by up-regulating expression of Bim and Bad. WA arrested GBM cells at the G2/M phase of the cell cycle through dephosphorylating Thr(161) of CDK1 by activating p53-independent p21 up-regulation. Knockdown of p21 restored cell cycle progression and cell viability by down-regulating the expression of Bad rather than Bim. We demonstrated that endoplasmic reticulum (ER) stress induced by WA through the
The import process for that PubMed record provides a complete abstract for me when I use the Zotero icon in my browser bar and also when I use the magic wand to bring the metadata into Zotero.
Please provide information about your Zotero version, browser and your operating system so that the experts here may offer help. Sorry that I could not be of more help.
[I tested your issue because I perform a daily extensive PubMed search that is an essential part of my work. I import selected records from the search results into my Zotero. Any new problem with PubMed imports would require me to take action.]
In addition to Zotero version, could you say how exactly you're importing, especially if that's not via the Save to Zotero button in the browser extension?
I just encountered the same problem with a Pubmed text file, which I imported using the import function from the file menu, as well as the import from clipboard function. Some abstracts are complete and some are truncated. I added some screenshots to my github gist. https://gist.github.com/michi-zuri/5750a395438492c6c32e30d667fa4174 Zotero version: 5.0.89 OS: macOS 10.13.6
This happens when lines in the abstract start with capital letters similar to Pubmed fields. We can try to see if we can fix this, but if at all possible I'd suggest using either Pubmed's XMLs, pubmed ID's, or Zotero's web importer to import these
Many thanks for opening the issue. Importing a batch of 1000 PMIDs through Zotero is rather slow in comparison to importing a file with all the content, so a solution would be great to have.
To be able to use my file anyway for now I found the following workaround inserting a soft hyphen before capital letters on new lines:
Open the file in atom code editor and find+replace with the following regex find: (^ )([A-Z][A-Z]) replace with: $1\u00AD$2
(except that atom does not support unicode characters, so you'd need to find a soft hyphen somewhere and copy/paste it to replace \u00AD in the above example.
After this, the newlines start with a soft hyphen instead of a set of capital letters and the abstracts (and titles and whatever other fields are affected) will not truncate anymore.
The problem occured specifically when a line in the import file did not start with a field tag, but still started with a capital letter or a number AND if that line also contained a hyphen. The whitespace that those wrapped lines contained was ignored. The fix now only considers subsequent lines as new fields if it doesn't start with whitespace.
@adamsmith : can you advice how users can benefit from the fix in the near future? Is any action required to update the translator file or will this be handled automatically? Does it depend on the Zotero version at all?
Zotero translators automatically update for all users within 24hs; no action needed (Versions of Zotero before 5.0 don't receive any updates of any kind, but hopefully most people aren't using those)
Upgrade Storage
Know that Oxford University Press journal articles' abstracts (in their metadata) are 'pre-truncated' by the publisher at a specified number of characters.
PMID- 31642559
OWN - NLM
STAT- MEDLINE
DCOM- 20200225
LR - 20200421
IS - 1365-2184 (Electronic)
IS - 0960-7722 (Print)
IS - 0960-7722 (Linking)
VI - 53
IP - 1
DP - 2020 Jan
TI - Withaferin A triggers G2/M arrest and intrinsic apoptosis in glioblastoma cells via
ATF4-ATF3-CHOP axis.
PG - e12706
LID - 10.1111/cpr.12706 [doi]
LID - e12706
AB - OBJECTIVE: Withaferin A (WA) is a bioactive compound with a remarkable anti-cancer
effect derived from Withania somnifera, commonly known as ashwagandha. However, the
anti-cancer mechanisms of WA in glioblastoma multiforme (GBM) are still unclear.
MATERIALS AND METHODS: Cell viability assays and xenografted nude mice were used to
evaluate the effects of WA, along with flow cytometry to detect apoptosis and cell
cycle of GBM. RNA-seq analysis, Western blotting, immunofluorescence staining,
qRT-PCR and siRNA gene silencing were carried out to determine the signalling
pathways affected by WA. RESULTS: Withaferin A significantly inhibited the growth of
GBM in vitro and in vivo and triggered the intrinsic apoptosis of GBM cells by
up-regulating expression of Bim and Bad. WA arrested GBM cells at the G2/M phase of
the cell cycle through dephosphorylating Thr(161) of CDK1 by activating
p53-independent p21 up-regulation. Knockdown of p21 restored cell cycle progression
and cell viability by down-regulating the expression of Bad rather than Bim. We
demonstrated that endoplasmic reticulum (ER) stress induced by WA through the
ATF4-ATF3-CHOP axis, initiated apoptosis and G2/M arrest in GBM cells. CONCLUSION:
We revealed a novel pathway that elucidated WA activation of apoptosis and G2/M
arrest in GBM cells through the ATF4-ATF3-CHOP axis. This discovery is important for
optimization of WA-based regimens for prevention and/or treatment of GBM.
CI - © 2019 The Authors. Cell Proliferation Published by John Wiley & Sons Ltd.
FAU - Tang, Qin
AU - Tang Q
AD - The State Key Laboratory of Bioactive Substance and Function of Natural Medicines,
Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union
Medical College, Beijing, China.
AD - Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica,
Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China.
FAU - Ren, Liwen
AU - Ren L
AD - The State Key Laboratory of Bioactive Substance and Function of Natural Medicines,
Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union
Medical College, Beijing, China.
AD - Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica,
Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China.
FAU - Liu, Jinyi
AU - Liu J
AD - The State Key Laboratory of Bioactive Substance and Function of Natural Medicines,
Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union
Medical College, Beijing, China.
AD - Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica,
Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China.
FAU - Li, Wan
AU - Li W
AD - The State Key Laboratory of Bioactive Substance and Function of Natural Medicines,
Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union
Medical College, Beijing, China.
AD - Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica,
Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China.
FAU - Zheng, Xiangjin
AU - Zheng X
AD - The State Key Laboratory of Bioactive Substance and Function of Natural Medicines,
Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union
Medical College, Beijing, China.
AD - Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica,
Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China.
FAU - Wang, Jinhua
AU - Wang J
AUID- ORCID: 0000-0001-8367-0787
AD - The State Key Laboratory of Bioactive Substance and Function of Natural Medicines,
Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union
Medical College, Beijing, China.
AD - Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica,
Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China.
FAU - Du, Guanhua
AU - Du G
AD - The State Key Laboratory of Bioactive Substance and Function of Natural Medicines,
Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union
Medical College, Beijing, China.
AD - Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica,
Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China.
LA - eng
GR - 2018ZX09711001-005-025/Technology Major Projects for "Major New Drugs Innovation and
Development"/
GR - 81573454/National Natural Science Foundation of China/
GR - 81703536/National Natural Science Foundation of China/
GR - 81703565/National Natural Science Foundation of China/
GR - 81803584/National Natural Science Foundation of China/
GR - 2016-I2M-3-007/CAMS Innovation Fund for Medical Sciences/
GR - 2018M640093/China Postdoctoral Science Foundation/
PT - Journal Article
DEP - 20191023
TA - Cell Prolif
JT - Cell proliferation
JID - 9105195
RN - 0 (ATF3 protein, human)
RN - 0 (ATF4 protein, human)
RN - 0 (Activating Transcription Factor 3)
RN - 0 (DDIT3 protein, human)
RN - 0 (Neoplasm Proteins)
RN - 0 (Withanolides)
RN - 145891-90-3 (Activating Transcription Factor 4)
RN - 147336-12-7 (Transcription Factor CHOP)
RN - L6DO3QW4K5 (withaferin A)
SB - IM
MH - Activating Transcription Factor 3/*metabolism
MH - Activating Transcription Factor 4/*metabolism
MH - Animals
MH - Cell Line, Tumor
MH - G2 Phase Cell Cycle Checkpoints/*drug effects
MH - Glioblastoma/*drug therapy/metabolism/pathology
MH - Humans
MH - M Phase Cell Cycle Checkpoints/*drug effects
MH - Mice
MH - Mice, Nude
MH - Neoplasm Proteins/genetics/*metabolism
MH - Signal Transduction/*drug effects
MH - Transcription Factor CHOP/*metabolism
MH - Withanolides/*pharmacology
MH - Xenograft Model Antitumor Assays
PMC - PMC6985693
OTO - NOTNLM
OT - apoptosis
OT - cell cycle
OT - endoplasmic reticulum
OT - glioblastoma
OT - unfolded protein response
COIS- The authors declare no conflicts of interest that pertain to this work.
EDAT- 2019/10/24 06:00
MHDA- 2020/02/26 06:00
CRDT- 2019/10/24 06:00
PHST- 2019/07/07 00:00 [received]
PHST- 2019/08/28 00:00 [revised]
PHST- 2019/09/20 00:00 [accepted]
PHST- 2019/10/24 06:00 [pubmed]
PHST- 2020/02/26 06:00 [medline]
PHST- 2019/10/24 06:00 [entrez]
AID - CPR12706 [pii]
AID - 10.1111/cpr.12706 [doi]
PST - ppublish
SO - Cell Prolif. 2020 Jan;53(1):e12706. doi: 10.1111/cpr.12706. Epub 2019 Oct 23.
Please provide information about your Zotero version, browser and your operating system so that the experts here may offer help. Sorry that I could not be of more help.
[I tested your issue because I perform a daily extensive PubMed search that is an essential part of my work. I import selected records from the search results into my Zotero. Any new problem with PubMed imports would require me to take action.]
https://gist.github.com/michi-zuri/5750a395438492c6c32e30d667fa4174
Zotero version: 5.0.89
OS: macOS 10.13.6
If you could please leave the gist in place so we have some sample data for testing a fix.
To be able to use my file anyway for now I found the following workaround inserting a soft hyphen before capital letters on new lines:
Open the file in atom code editor and find+replace with the following regex
find: (^ )([A-Z][A-Z])
replace with: $1\u00AD$2
(except that atom does not support unicode characters, so you'd need to find a soft hyphen somewhere and copy/paste it to replace \u00AD in the above example.
After this, the newlines start with a soft hyphen instead of a set of capital letters and the abstracts (and titles and whatever other fields are affected) will not truncate anymore.
The problem occured specifically when a line in the import file did not start with a field tag, but still started with a capital letter or a number AND if that line also contained a hyphen. The whitespace that those wrapped lines contained was ignored. The fix now only considers subsequent lines as new fields if it doesn't start with whitespace.
@adamsmith : can you advice how users can benefit from the fix in the near future? Is any action required to update the translator file or will this be handled automatically? Does it depend on the Zotero version at all?