Upgrade StorageFrom Bibdesk to Zotero with arXive
Hi,
I'm trying to migrate from Bibdesk to Zotero. I have 3 problems:
1- save the manual classification in Bibdesk using static groups into Zotero tags;
2- migrate arXive papers;
3- migrate the associated PDFs.
1- If I simply have Zotero read the Bibdesk .bib file, I loose all the classification. I can select the papers in each group, copy their bibdesk records to the clipbord, import them into Zotero with "Import from clipbord", and assign to these files a new tag corresponding to the old static group. Then I can remove the duplicate files for the papers originally part of ore than one static group. I have a few tens of group, the procedure in boring but possible. Is there a quicker way to do it?
2- the problem in doing this is that most of my papers come from arXive and they have entries like this in the .bib file:
@article{Berg19,
Abstract = {Some Test.},
Adscomment = {8 pages, 3 figures, resubmitted to ApJL, comments welcome},
Adsnote = {Provided by the SAO/NASA Astrophysics Data System},
Adsurl = {https://ui.adsabs.harvard.edu/abs/2019arXiv190506434B},
Archiveprefix = {arXiv},
Arxivurl = {http://arxiv.org/abs/1905.06434},
Author = {{Berg}, D.~A. and {Chisholm}, J. and {Erb}, D.~K. and {Pogge}, R. and {Henry}, A. and {Olivier}, G.~M.},
Date-Added = {2019-05-28 09:31:34 +0200},
Date-Modified = {2019-05-28 09:31:36 +0200},
Eprint = {1905.06434},
Journal = {arXiv e-prints},
Keywords = {Astrophysics - Astrophysics of Galaxies},
Month = may,
Read = {0},
Title = {{Intense CIV and HeII Emission in z\~{}0 Galaxies}},
Year = 2019,
Bdsk-File-1 = {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},
Bdsk-Url-1 = {http://arxiv.org/abs/1905.06434},
Bdsk-Url-2 = {https://ui.adsabs.harvard.edu/abs/2019arXiv190506434B}}
When importing this into Zotero, all the data on the reference are lost, the arXive number is only saved in the Extra field: "_eprint: 1905.06434" and it is difficult to retrive from here for many papers (I cannot click the Zotero entry and load the arXive page). Is it possible to save the URLs and access them by a simple click?
3- Is there a easy way to trasfer the pdf? I see many discussions but at the end I'm not sure what is the best way. I my case I could avoid loading all the pdf if there is a easy way to access my papers by simply clicking on them, see the previous point.
Thanks
I'm trying to migrate from Bibdesk to Zotero. I have 3 problems:
1- save the manual classification in Bibdesk using static groups into Zotero tags;
2- migrate arXive papers;
3- migrate the associated PDFs.
1- If I simply have Zotero read the Bibdesk .bib file, I loose all the classification. I can select the papers in each group, copy their bibdesk records to the clipbord, import them into Zotero with "Import from clipbord", and assign to these files a new tag corresponding to the old static group. Then I can remove the duplicate files for the papers originally part of ore than one static group. I have a few tens of group, the procedure in boring but possible. Is there a quicker way to do it?
2- the problem in doing this is that most of my papers come from arXive and they have entries like this in the .bib file:
@article{Berg19,
Abstract = {Some Test.},
Adscomment = {8 pages, 3 figures, resubmitted to ApJL, comments welcome},
Adsnote = {Provided by the SAO/NASA Astrophysics Data System},
Adsurl = {https://ui.adsabs.harvard.edu/abs/2019arXiv190506434B},
Archiveprefix = {arXiv},
Arxivurl = {http://arxiv.org/abs/1905.06434},
Author = {{Berg}, D.~A. and {Chisholm}, J. and {Erb}, D.~K. and {Pogge}, R. and {Henry}, A. and {Olivier}, G.~M.},
Date-Added = {2019-05-28 09:31:34 +0200},
Date-Modified = {2019-05-28 09:31:36 +0200},
Eprint = {1905.06434},
Journal = {arXiv e-prints},
Keywords = {Astrophysics - Astrophysics of Galaxies},
Month = may,
Read = {0},
Title = {{Intense CIV and HeII Emission in z\~{}0 Galaxies}},
Year = 2019,
Bdsk-File-1 = {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},
Bdsk-Url-1 = {http://arxiv.org/abs/1905.06434},
Bdsk-Url-2 = {https://ui.adsabs.harvard.edu/abs/2019arXiv190506434B}}
When importing this into Zotero, all the data on the reference are lost, the arXive number is only saved in the Extra field: "_eprint: 1905.06434" and it is difficult to retrive from here for many papers (I cannot click the Zotero entry and load the arXive page). Is it possible to save the URLs and access them by a simple click?
3- Is there a easy way to trasfer the pdf? I see many discussions but at the end I'm not sure what is the best way. I my case I could avoid loading all the pdf if there is a easy way to access my papers by simply clicking on them, see the previous point.
Thanks
https://forums.zotero.org/discussion/81158/import-pdfs-linked-in-bibdesk-file-into-zotero
You could try the steps there and follow up in that discussion in case things are unclear.
I'm currently migrating in this way:
- in Bibdesk I select the papers of a tematic gruop ("TOPIC");
- create a Bibliography.bib file with these files;
- stream edit this file to change "keywords" and "Url":
>> sed 's/.*Keywords.*/Keywords = {TOPIC}/g' Bibliography.bib > bib2.bib
>> sed 's/Adsurl/Url/g' bib2.bib > TOPIC.bib
- import thi TOPIC.bib file into Zotero;
- merge the duplicated papers that in Bibdesk are part of more than one group;
- load only the pdf I need (I had more then 6000 pdfs in Bibdesk, for more than 12GB, I don't want to move all of them).