CDR Tickets

Issue Number 3261
Summary [Citation] Non journal Pubmed citation import error
Created 2010-11-03 14:50:15
Issue Type Improvement
Submitted By Osei-Poku, William (NIH/NCI) [C]
Assigned To Kline, Bob (NIH/NCI) [C]
Status Closed
Resolved 2010-11-18 16:07:33
Resolution Won't Fix
Path /home/bkline/backups/jira/ocecdr/issue.107589
Description

BZISSUE::4951
BZDATETIME::2010-11-03 14:50:15
BZCREATOR::William Osei-Poku
BZASSIGNEE::Bob Kline
BZQACONTACT::William Osei-Poku

When importing certain citations which appear to be non journal citations (books and documents), users get the following errors:

"article not found"

Example is PMID 20301715 which users eventually created the following CDR document CDR0000687576.

The others are:
PPMID 20301295
PMID: 20301779

Would you be able to fix the errors so that we can import these citations?

Comment entered 2010-11-03 14:50:54 by Osei-Poku, William (NIH/NCI) [C]

BZDATETIME::2010-11-03 14:50:54
BZCOMMENTOR::William Osei-Poku
BZCOMMENT::1

Changed QA from Lakshmi

Comment entered 2010-11-04 10:44:05 by Kline, Bob (NIH/NCI) [C]

BZDATETIME::2010-11-04 10:44:05
BZCOMMENTOR::Bob Kline
BZCOMMENT::2

What the software is looking for (in fact, I checked all the way back to the original version of the program in 2001) is the 'PubmedArticle' element. What it's getting instead for the citations you identified above is a 'PubmedBookArticle' element. Is this a change that NLM slipped in under the radar, or is this a change in our requirements? If the latter, just out of curiosity - what triggered the need to import non-journal citations after all these years instead of entering them as PDQCitations? It's customary when requesting a change in requirements which have been in place this long to provide some background information explaining the need for the change.

Comment entered 2010-11-04 11:45:49 by Kline, Bob (NIH/NCI) [C]

BZDATETIME::2010-11-04 11:45:49
BZCOMMENTOR::Bob Kline
BZCOMMENT::3

I went back and dug out the original requirements for Citation import. Here's what it says:

"Citation records for the CDR will be maintained in two ways:

· record extraction from PUBMED

    • citations for articles published in journals indexed by MEDLINE

· creation of records in the editor

    • citations for articles published in journals not indexed by MEDLINE

    • Citations for books and book chapters

    • Citations for websites, online publications"

[From reqscurrent.xls attachment to email message from Eileen Bator sent 2001-09-11]

Comment entered 2010-11-05 18:04:53 by Juthe, Robin (NIH/NCI) [E]

BZDATETIME::2010-11-05 18:04:53
BZCOMMENTOR::Robin Juthe
BZCOMMENT::4

Here's some background Bob. I believe what is new here is that these documents (all GeneReviews online summaries) are now available in PubMed and were not previously. I think it's okay to create citation records for these since there are only 3 so far and they aren't commonly cited, but if it becomes a more frequent issue, then we may want to talk about changing the requirements in order to import them from PubMed.

Comment entered 2010-11-12 12:03:54 by Osei-Poku, William (NIH/NCI) [C]

BZDATETIME::2010-11-12 12:03:54
BZCOMMENTOR::William Osei-Poku
BZCOMMENT::5

We discussed this issue with Margaret in the CIAT review meeting on Tuesday, so I will keep it open until we discuss it in the next CDR meeting.

Comment entered 2010-11-18 16:07:33 by Kline, Bob (NIH/NCI) [C]

BZDATETIME::2010-11-18 16:07:33
BZCOMMENTOR::Bob Kline
BZCOMMENT::6

Since the current behavior conforms to the original requirements, and the number of anticipated cases to be entered as PDQ Citations is low, we agreed that at this point it's best to leave the software as it is.

Elapsed: 0:00:00.001671