Medline format
First of all, thank you for zotero! It seems a dream come true.
My point is I work a lot with references in PubMed/Medline format. By now I do some twists to put it into zotero using scripts before but this is sometimes a cumbersome task. I don't see I can do this straightforward in zotero. Any idea?
Thank you!
My point is I work a lot with references in PubMed/Medline format. By now I do some twists to put it into zotero using scripts before but this is sometimes a cumbersome task. I don't see I can do this straightforward in zotero. Any idea?
Thank you!
Anyway, do you know how to put Medline format into Zotero? A bit more ambitious question is, do you think it's worth Zotero can do this in the future?
Thank you!
--
Abel
If you have or can get the medline xml format, bibutils is an excellent set of programs that can convert to MODS XML (which Zotero can import) or, from that bibtex/ris (which Zotero can also import).
However, AFAIK the Bibutils 'med2xml' tool requires PubMed XML as input data. If you're dependent on the MEDLINE format (i.e. somehow can't refetch your data in PubMed XML format), then you could also use the refbase demo database for conversion of MEDLINE-formatted records into, say, RIS format, then import the RIS data into Zotero. To do so:
1. Login at the refbase demo database
2. Import your MEDLINE data via the import page
3. Display all your imported data on a single page (using the display options at the top right of the screen)
4. Select all records and click on the "Export" button at the bottom of the page (with "RIS" selected from the dropdown menu)
5. Choose the downloaded file when importing into Zotero
Regards,
This Perl script --included in the References bibliographic tools (RBT)-- does a clean translation from PubMed/Medline to BibTex. You can get it from
http://prdownloads.sourceforge.net/references/rbt03.zip?download
BTW you'll find it in the References home page, it's worth seeing at http://prdownloads.sourceforge.net/
Unfortunately, for snapshoting pdfs of these articles you have to create additional entries andd copy their URL into the URL field of the entry that contains the references. In addition, right clicking and and snapshoting links to pdfs doesn't work for all journals. In these cases one has to store the pdf locally first and open the pdf in firefox. One the has to make a snapshot and copy the URL to the entry with the reference.
I mainly work with articles from Medline and been trying to import them to Zotero directly without success.
I found this link http://www.zotero.org/translators/ where it says that Medline should be compatible through Ebsco and linking there, the link only goes to a "file not found (404)" page though.
Anyone knows anything more about this?
First you need to clean-up your MEDLINE file using Find/Replace command from a text editor or writing a script.
- Remove all fields except for PMID.
- Append "[uid]" after the PMID, e.g. 1234567[uid]. (This is required for multiple search)
- Connect each PMID using (space)OR(space). (Remove line breaks)
You should have a file reads like this:
PMID_1[uid] OR PMID_2[uid] OR ... OR PMID_n[uid]
Then copy and paste this string into PubMed search field.
Now you can import all references into Zotero by clicking a folder icon in the location bar. Be aware that you can export only you see on a single page (20 by default). If necessary, increase the number in "show" tab. Your Firefox may hung up (or take infinite time to be done) if you try to import too many references at once.
If not, is there a way for me to create an export script to do so? Although I'm very new to Zotero I am familiar with converting bib formats. I can currently create the XML file by 1) exporting from Zotero into RIS format, 2) importing the file into Reference Manager 3) using a self-created script to export into a text file that is almost the right format, and finally 4) using PowerGrep to automatically manipulate the text file into the exact XML format. This is not only tedious and time-consuming but, because Reference Manager isn't UTF-8 friendly, I have character problems.
Thanks
Thank you.
Thanks a lot Fabre!
Here's the way i use it:
Once i found the article(s) I want i choose show as Medline.
Search the page for pmid and cut and paste the number just after that into a new window, end with [uid] just like Fabre described it and put OR between each entry if you're looking up more than one article. Voilá! just add as references the usual way andabstract author etc is instantly registered in zotero :)
If im going to convert an entire collection though, I find using the perlscrip as described above more convenient.
Do you mean the Notes icon in the Zotero toolbar?
I selected (i.e checked the box or highligthed) a reference found in Hubmed and clicked the notes icon but that didn't work.
Please advise.
Thanks
http://www.zotero.org/support/getting_stuff_into_your_library#automatically_capture_bibliographic_information_from_the_web
Work fine with PubMed as well.
I'm utterly new to all of this so I could definitely use some informed guidance...
Cheers in advance,
chris
1. Place your search term in the box on www.ncbi.nlm.nih/pubmed/
2. When you have the listing of references tick at left those titles you need in your Zotero library
3. Click on Send To (top, right), choose File, and in the Format drop-down menu click on XML. Create the file and save it to your hard disk.
4. Open Zotero and click on the cogwheel
5. Choose Import, find your .xml file on the disk and let it roll
6. You should find your references listed under a collection bearing the name of the file saved on your hard disk
"My point is I work a lot with references in PubMed/Medline format. By now I do some twists to put it into zotero using scripts before but this is sometimes a cumbersome task. I don't see I can do this straightforward in zotero. Any idea?"
Search in the Zotero Styles Repository the "National Library of Medicine" style (
https://www.zotero.org/styles/national-library-of-medicine-grant-proposals)