| Issue Number | 528 |
|---|---|
| Summary | Citations Import from NLM |
| Created | 2019-11-25 12:36:37 |
| Issue Type | Improvement |
| Submitted By | Osei-Poku, William (NIH/NCI) [C] |
| Assigned To | Kline, Bob (NIH/NCI) [C] |
| Status | Closed |
| Resolved | 2020-03-06 16:59:51 |
| Resolution | Fixed |
| Path | /home/bkline/backups/jira/oceebms/issue.252799 |
Cynthia and Minaxi brought to my attention that there was a new PubMed release on November 18, 2019 which has introduced a new text format called RIS, for generating text files of results in MEDLINE format. Since this would be used to import search results into the EBMS it may not work with the current setup. The legacy PubMed system will be available until April 2020 after which this new version will be the only version available. Could you please investigate this new format to see its possible impact? Alternatively, we could revisit importing citations using PubMed IDs as has been suggested in the past.
https://www.nlm.nih.gov/pubs/techbull/nd19/nd19_pubmed_new.html
Tagging ~juther , ~mbeckwit , ~boggessc and ~trivedim
Below is email response form NLM support.
From: NLM Support <nlm-support@nlm.nih.gov>
Sent: Friday, November 22, 2019 1:20 PM
To: Boggess, Cynthia <Cynthia.Boggess@icf.com>
Subject: Re: case #CAS-454649-S6F1C2: Medline format for creating text
files TRACKING:000427000001120
Hi Cynthia,
Thank you for trying the new PubMed and taking the time to send us your feedback. All comments are being reviewed by the PubMed team and will be used to help inform the ongoing development of PubMed.
In the new PubMed, MEDLINE format is replaced by RIS to improve interoperability of the data with other systems such as reference management software. We plan to further augment the RIS download with additional fields in a future update.
The new PubMed is under active development, and features will be introduced and updated on a regular basis as we continue to enhance the system. We are continuing to prioritize features based on user research, including usability testing and feedback from users.
To learn more about the new site, please watch our recent webinar: A New PubMed: Highlights for Information Professionals: https://www.nlm.nih.gov/oet/ed/pubmed/events/2019_09.html
For the latest updates and announcements, please see the NLM Technical Bulletin: https://www.nlm.nih.gov/pubs/techbull.
Kind regards,
Jessica
Jessica Chan, MLIS (Contractor)
National Center for Biotechnology Information
U.S. National Library of Medicine
Not to say we shouldn't add support for the new system in time for the launch, but I did want to point out that NLM says:
Our legacy PubMed system will be available for some months following the launch.
Also interesting (as a side note) is that the new PubMed's front end is built using a Python web framework, so we're in good company. :-)
Documentation for the RIS format:
Ready for testing on EBMS DEV.
As part of this ticket, I am switching over the links to PubMed to send users to the new PubMed, on the assumption that the old URLs will eventually go away. Let me know if you don't want this.
Minaxi and I have tested the RIS file importing and it seems to be working just fine. We noticed that the RIS file does not have a limit to 200 citations like the MEDLINE files so that will make importing easier and a bit quicker.
I also noticed that the error message that appears on the import page when an unsupported file is used needs to be updated to instruct users to use the new RIS format.
From Minaxi (below).
From: Trivedi, Minaxi <Minaxi.Trivedi@icf.com>
Sent: Thursday, March 5, 2020 9:45 AM
To: Boggess, Cynthia <Cynthia.Boggess@icf.com>; Osei-Poku, William
<William.Osei-Poku@icf.com>
Subject: RE: Biscayne UAT [was: Re: CDR/EBMS Status Meeting]
I could log in to the EBMS without getting any error.
I tested importing two files in RIS format and it works fine.
Thanks,
Minaxi
Error message updated to refer to the new format.
Verified on QA, including the updated error message.
~oseipokuw - does this still need more testing?
I think this can be closed. With a few unrelated exceptions, we've been importing citations fine using the current format.
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