Upgrade StorageUnable to get PDFs stored on computer into Zotero Standalone
Hello,
I've previously used Mendeley but would like to give Zotero a try. However, I've tried importing the library of PDFs stored on my computer in multiple ways, none of which have worked.
1) I tried importing from Mendeley as a .bib file. Parent files were created but the linked PDFs weren't included. I tried the following based on previous forum discussion:
a) Replacing "file = {:" with "pdf = {" and deleting ":PDF" in the .bib file as recommended here: https://forums.zotero.org/discussion/6527/
b) Deleting ":C$\backslash$:" as recommended here: https://forums.zotero.org/discussion/23775/error-when-trying-to-import-data-to-zotero-bib-or-ris/
None of these worked - Zotero only imported the info for each reference, not the linked PDF file.
2) Importing from Mendeley as .ris didn't get anywhere with Zotero, an error popped up and nothing was imported.
3) I instead tried simply dragging and dropping my collection of PDFs into Zotero. Unfortunately this also didn't work. Sometimes, the Standalone application thinks for a moment and adds a couple PDFs (out of 100+). Sometimes it adds only one. Sometimes it doesn't add any.
I just want to get my PDFs into Zotero - how can I do this?
Thanks.
I've previously used Mendeley but would like to give Zotero a try. However, I've tried importing the library of PDFs stored on my computer in multiple ways, none of which have worked.
1) I tried importing from Mendeley as a .bib file. Parent files were created but the linked PDFs weren't included. I tried the following based on previous forum discussion:
a) Replacing "file = {:" with "pdf = {" and deleting ":PDF" in the .bib file as recommended here: https://forums.zotero.org/discussion/6527/
b) Deleting ":C$\backslash$:" as recommended here: https://forums.zotero.org/discussion/23775/error-when-trying-to-import-data-to-zotero-bib-or-ris/
None of these worked - Zotero only imported the info for each reference, not the linked PDF file.
2) Importing from Mendeley as .ris didn't get anywhere with Zotero, an error popped up and nothing was imported.
3) I instead tried simply dragging and dropping my collection of PDFs into Zotero. Unfortunately this also didn't work. Sometimes, the Standalone application thinks for a moment and adds a couple PDFs (out of 100+). Sometimes it adds only one. Sometimes it doesn't add any.
I just want to get my PDFs into Zotero - how can I do this?
Thanks.
@article{Yamanaka2006,
abstract = {In insects, steroid hormones named ecdysteroids elicit molting and metamorphosis. The prothoracic gland (PG) is a predominant source of ecdysteroids, where their biosynthesis (ecdysteroidogenesis) is regulated by several neuropeptides. Here, we report that FMRFamide-related peptides (FaRPs) regulate ecdysteroidogenesis through direct innervation of the PG in the silkworm Bombyx mori. We purified a previously uncharacterized Bombyx FaRP, DPSFIRFamide, and identified the corresponding Bombyx FMRFamide gene (Bommo-FMRFamide, BRFa), which encodes three additional FaRPs. All BRFa peptides suppressed ecdysteroidogenesis in the PG by reducing cAMP production by means of the receptor for Bommo-myosuppressin, another FaRP we have previously shown to act as a prothoracicostatic factor. BRFa is predominantly expressed in neurosecretory cells of thoracic ganglia, and the neurons in the prothoracic ganglion innervate the PG to supply all four peptides to the gland surface. Electrophysiological recordings during development confirmed the increased firing activity of BRFa neurons in stages with low PG activity and decreased ecdysteroid levels in the hemolymph. To our knowledge, this study provides the first report of peptides controlling ecdysteroidogenesis by direct innervation.},
author = {Yamanaka, Naoki and Zitnan, Dusan and Kim, Young-Joon and Adams, Michael E and Hua, Yue-Jin and Suzuki, Yusuke and Suzuki, Minoru and Suzuki, Akemi and Satake, Honoo and Mizoguchi, Akira and Asaoka, Kiyoshi and Tanaka, Yoshiaki and Kataoka, Hiroshi},
doi = {10.1073/pnas.0511196103},
file = {:C$\backslash$:/Users/Davis/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Yamanaka et al. - 2006 - Regulation of insect steroid hormone biosynthesis by innervating peptidergic neurons.pdf:pdf},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
keywords = {Amino Acid Sequence,Animals,Bombyx,Bombyx: metabolism,FMRFamide,FMRFamide: chemistry,FMRFamide: genetics,FMRFamide: isolation \& purification,FMRFamide: metabolism,Ganglia,Ganglia: metabolism,Gene Expression Regulation, Developmental,Humans,Insect Hormones,Insect Hormones: biosynthesis,Molecular Sequence Data,Neurons,Neurons: cytology,Neurons: metabolism,RNA, Messenger,RNA, Messenger: genetics,RNA, Messenger: metabolism},
month = jun,
number = {23},
pages = {8622--7},
pmid = {16707581},
title = {{Regulation of insect steroid hormone biosynthesis by innervating peptidergic neurons.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1482630\&tool=pmcentrez\&rendertype=abstract},
volume = {103},
year = {2006}
}
could you try if this works if you delete
"C$\backslash$:" entirely? Try with just one entry for testing - that either works or it doesn't.
I tried deleting "C$\backslash$:" and it still didn't import the linked PDF.
or even better yet, maybe I could convince @aurimasv, who actually uses Windows, to do that.
Might take a little.
I think Zotero can handle them when they're in the right format (which they're definitely not coming from Mendeley), but someone has to look at that in Windows.
Here's how: place the bibtex output file into a folder that's a parent of Mendeley's PDF storage folder. It looks like "Mendeley Desktop" would be a good candidate above.
Then cut off the entire filepath up to and including that folder in the file (obviously you can do that via search and replace). The filepaths line above should look like this:
file = {:Downloaded/Yamanaka et al. - 2006 - Regulation of insect steroid hormone biosynthesis by innervating peptidergic neurons.pdf:pdf},
Note that there is _no_ slash or backslash in before the first folder. Zotero should now import all PDFs from Mendeley.
I'm also interested in the RIS import that failed for you. Could you post a sample RIS entry? Hopefully one that fails to import.
Regarding the issue with dragging and dropping PDFs in, it is indeed rather slow now and the devs are working on improving Zotero performance, so this is likely to become faster in the future. I dragged and dropped 400 PDFs and it took about 2 minutes to import, but all of them were imported. There is currently an issue where if the PDF file name is very long (and becomes too long to store in your file system within the Zotero directory) it is silently dropped. This may be what is happening to you. We're aware of the issue and it should be fixed soon.
Here is an example of what I changed it to:
@article{Thor2002,
abstract = {Motor neuron differentiation has been studied intensively in both invertebrates and vertebrates in recent years. These studies have led to the identification of several key regulatory genes acting to generate motor neurons and to specify their subclass identities. By comparing findings from Caenorhabditis elegans, Drosophila and vertebrate model systems, it is apparent that both evolutionarily conserved and non-conserved mechanisms are used.},
author = {Thor, Stefan and Thomas, JB},
file = {:Downloaded/Thor, Thomas - 2002 - Motor neuron specification in worms, flies and mice conserved and 'lost'mechanisms.pdf:pdf},
issn = {0959-437X},
journal = {Current opinion in genetics \& development},
keywords = {Animals,Biological Evolution,Caenorhabditis elegans,Caenorhabditis elegans: cytology,Caenorhabditis elegans: embryology,Caenorhabditis elegans: genetics,Conserved Sequence,Developmental,Drosophila melanogaster,Drosophila melanogaster: cytology,Drosophila melanogaster: embryology,Drosophila melanogaster: genetics,Gene Expression Regulation,Homeodomain Proteins,Homeodomain Proteins: physiology,Mice,Motor Neurons,Motor Neurons: physiology,Species Specificity,Vertebrates,Vertebrates: embryology,Vertebrates: genetics},
month = oct,
number = {5},
pages = {558--64},
pmid = {12200161},
title = {{Motor neuron specification in worms, flies and mice: conserved and 'lost'mechanisms}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/12200161 http://www.sciencedirect.com/science/article/pii/S0959437X02003404},
volume = {12},
year = {2002}
}
When trying to import this single document to Zotero I didn't get the error but it again didn't include the linked PDF.
TY - JOUR
T1 - Regulation of insect steroid hormone biosynthesis by innervating peptidergic neurons.
A1 - Yamanaka, Naoki
A1 - Zitnan, Dusan
A1 - Kim, Young-Joon
A1 - Adams, Michael E
A1 - Hua, Yue-Jin
A1 - Suzuki, Yusuke
A1 - Suzuki, Minoru
A1 - Suzuki, Akemi
A1 - Satake, Honoo
A1 - Mizoguchi, Akira
A1 - Asaoka, Kiyoshi
A1 - Tanaka, Yoshiaki
A1 - Kataoka, Hiroshi
Y1 - 2006/06//
KW - Amino Acid Sequence
KW - Animals
KW - Bombyx
KW - Bombyx: metabolism
KW - FMRFamide
KW - FMRFamide: chemistry
KW - FMRFamide: genetics
KW - FMRFamide: isolation & purification
KW - FMRFamide: metabolism
KW - Ganglia
KW - Ganglia: metabolism
KW - Gene Expression Regulation, Developmental
KW - Humans
KW - Insect Hormones
KW - Insect Hormones: biosynthesis
KW - Molecular Sequence Data
KW - Neurons
KW - Neurons: cytology
KW - Neurons: metabolism
KW - RNA, Messenger
KW - RNA, Messenger: genetics
KW - RNA, Messenger: metabolism
JF - Proceedings of the National Academy of Sciences of the United States of America
VL - 103
IS - 23
SP - 8622
EP - 7
DO - 10.1073/pnas.0511196103
UR - http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1482630&tool=pmcentrez&rendertype=abstract
L1 - file:///C:/Documents and Settings/Davis Sam/My Documents/Dropbox/Allan Lab/3.pdf
N2 - In insects, steroid hormones named ecdysteroids elicit molting and metamorphosis. The prothoracic gland (PG) is a predominant source of ecdysteroids, where their biosynthesis (ecdysteroidogenesis) is regulated by several neuropeptides. Here, we report that FMRFamide-related peptides (FaRPs) regulate ecdysteroidogenesis through direct innervation of the PG in the silkworm Bombyx mori. We purified a previously uncharacterized Bombyx FaRP, DPSFIRFamide, and identified the corresponding Bombyx FMRFamide gene (Bommo-FMRFamide, BRFa), which encodes three additional FaRPs. All BRFa peptides suppressed ecdysteroidogenesis in the PG by reducing cAMP production by means of the receptor for Bommo-myosuppressin, another FaRP we have previously shown to act as a prothoracicostatic factor. BRFa is predominantly expressed in neurosecretory cells of thoracic ganglia, and the neurons in the prothoracic ganglion innervate the PG to supply all four peptides to the gland surface. Electrophysiological recordings during development confirmed the increased firing activity of BRFa neurons in stages with low PG activity and decreased ecdysteroid levels in the hemolymph. To our knowledge, this study provides the first report of peptides controlling ecdysteroidogenesis by direct innervation.
ER -
I tried importing only 1 or 2 .ris files at a time to Zotero, and that worked. But importing 10 at a time didn't.
paste it into and empty notepad file, shorten the filepath as per above, save it into the Mendeley Desktop folder and see if import works.
If it doesn't, please post the bibtex with the shortened filepath here.
@article{Yamanaka2006,
abstract = {In insects, steroid hormones named ecdysteroids elicit molting and metamorphosis. The prothoracic gland (PG) is a predominant source of ecdysteroids, where their biosynthesis (ecdysteroidogenesis) is regulated by several neuropeptides. Here, we report that FMRFamide-related peptides (FaRPs) regulate ecdysteroidogenesis through direct innervation of the PG in the silkworm Bombyx mori. We purified a previously uncharacterized Bombyx FaRP, DPSFIRFamide, and identified the corresponding Bombyx FMRFamide gene (Bommo-FMRFamide, BRFa), which encodes three additional FaRPs. All BRFa peptides suppressed ecdysteroidogenesis in the PG by reducing cAMP production by means of the receptor for Bommo-myosuppressin, another FaRP we have previously shown to act as a prothoracicostatic factor. BRFa is predominantly expressed in neurosecretory cells of thoracic ganglia, and the neurons in the prothoracic ganglion innervate the PG to supply all four peptides to the gland surface. Electrophysiological recordings during development confirmed the increased firing activity of BRFa neurons in stages with low PG activity and decreased ecdysteroid levels in the hemolymph. To our knowledge, this study provides the first report of peptides controlling ecdysteroidogenesis by direct innervation.},
author = {Yamanaka, Naoki and Zitnan, Dusan and Kim, Young-Joon and Adams, Michael E and Hua, Yue-Jin and Suzuki, Yusuke and Suzuki, Minoru and Suzuki, Akemi and Satake, Honoo and Mizoguchi, Akira and Asaoka, Kiyoshi and Tanaka, Yoshiaki and Kataoka, Hiroshi},
doi = {10.1073/pnas.0511196103},
file = {:Downloaded/Yamanaka et al. - 2006 - Regulation of insect steroid hormone biosynthesis by innervating peptidergic neurons.pdf:pdf},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
keywords = {Amino Acid Sequence,Animals,Bombyx,Bombyx: metabolism,FMRFamide,FMRFamide: chemistry,FMRFamide: genetics,FMRFamide: isolation \& purification,FMRFamide: metabolism,Ganglia,Ganglia: metabolism,Gene Expression Regulation, Developmental,Humans,Insect Hormones,Insect Hormones: biosynthesis,Molecular Sequence Data,Neurons,Neurons: cytology,Neurons: metabolism,RNA, Messenger,RNA, Messenger: genetics,RNA, Messenger: metabolism},
month = jun,
number = {23},
pages = {8622--7},
pmid = {16707581},
title = {{Regulation of insect steroid hormone biosynthesis by innervating peptidergic neurons.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1482630\&tool=pmcentrez\&rendertype=abstract},
volume = {103},
year = {2006}
}
/Users/Davis/AppData/... really looks like a Mac filepath (except for the C:\ at the beginning). Does that filepath actually exist on your computer? Does it have the PDF?
Yamanaka et al. - 2006 - Regulation of insect steroid hormone biosynthesis by innervating peptidergic neurons.pdf - is actually in the folder "Downloaded"?
I'd be pretty sure that the RIS import failed for the same reason, the RIS above looks very clean and I know of other people who've imported their Mendeley libraries via RIS recently.
I don't know enough about Zotero's file handling, so Aurimas or Simon would have to take it from here.
Also, when you say importing 10 at a time didn't work, what do you mean by "didn't work"? Was there an error? Did Zotero freeze? Nothing happened?
Can you tell me how to fix this?
Thanks,
Steve Jenkins
Set the launchNonNative Files hidden preference to true:
http://www.zotero.org/support/preferences/hidden_preferences
@incollection{Carlson2005b,
address = {New York},
author = {Carlson, Jon and Watts, Richard E. and Maniacci, Michael},
booktitle = {Adlerian Therapy: Theory and Practice},
file = {:Downloaded/Carlson, Watts, Maniacci - 2005 - 2I - Brief Couples Therapy.pdf:pdf},
keywords = {Adlerian Therapy,Brief Psychotherapy,Couples Therapy,Individual Psychology},
mendeley-tags = {Adlerian Therapy,Brief Psychotherapy,Couples Therapy,Individual Psychology},
publisher = {American Psychological Association},
title = {{2I - Brief Couples Therapy}},
year = {2005}
}