CDR Tickets

Issue Number 3262
Summary [Citation] Possible citation schema changes for 2011
Created 2010-11-15 11:03:04
Issue Type Improvement
Submitted By Osei-Poku, William (NIH/NCI) [C]
Assigned To Kline, Bob (NIH/NCI) [C]
Status Closed
Resolved 2011-01-18 11:18:07
Resolution Fixed
Path /home/bkline/backups/jira/ocecdr/issue.107590
Description

BZISSUE::4952
BZDATETIME::2010-11-15 11:03:04
BZCREATOR::William Osei-Poku
BZASSIGNEE::Bob Kline
BZQACONTACT::William Osei-Poku

I am creating this issue to take care of possible changes to the citations schema due to future changes announced by PubMed for 2011. We will provide a list of elements that are likely to be affected by these changes.

-Below is a summary of the changes emailed by Bob-

---Original Message---
From: Bob Kline bkline@rksystems.com
Sent: Tuesday, September 14, 2010 4:34 PM
To: Margaret Beckwith; Osei-Poku, William
Subject: Heads-up for citation changes effective in 2011

Here's what NLM says will change on January 1:

a. Changed nlmmedlinecitationset_100101.dtd to
nlmmedlinecitationset_110101.dtd.
b. Added Label and NlmCategory attributes to AbstractText.
c. Added element SupplMeshList to MedlineCitation.
d. Added element SupplMeshName with Type attribute to
SupplMeshList.
e. Added Type attribute to DescriptorName.
f. Added VersionID and VersionDate attributes to MedlineCitation.
g. Added Version attribute to PMID.
h. Repositioned NameID element in Author.
i. Changed NameID Source attribute to unspecified values.
j. Added new Owner attribute valid value NLM-AUTO.


Bob Kline
http://www.rksystems.com
mailto:bkline@rksystems.com

Comment entered 2010-11-15 11:06:12 by Osei-Poku, William (NIH/NCI) [C]

BZDATETIME::2010-11-15 11:06:12
BZCOMMENTOR::William Osei-Poku
BZCOMMENT::1

I have attached another email from PubMed forwarded to us by Bob.

Comment entered 2010-11-15 11:06:12 by Osei-Poku, William (NIH/NCI) [C]

Attachment Citation changes.doc has been added with description: Email from PubMed

Comment entered 2010-11-22 10:44:47 by Kline, Bob (NIH/NCI) [C]

BZDATETIME::2010-11-22 10:44:47
BZCOMMENTOR::Bob Kline
BZCOMMENT::2

We decided in this past Thursday's meeting that we would wait until the changes are actually in place at NLM and a citation import fails.

Comment entered 2010-12-14 09:44:26 by Osei-Poku, William (NIH/NCI) [C]

BZDATETIME::2010-12-14 09:44:26
BZCOMMENTOR::William Osei-Poku
BZCOMMENT::3

It looks like PubMed has started implementing the schema changes.

Users have started getting the following error message while importing citations:

“*Imported with errors* Publishable version not created. Unexpected attribute version =‘1’ in element PMID.”

This appears to be related to items "f" and "g" below.

It seems the above error message is not the only one. I will see if I can find the other error message(s).

Here is the list of affected Citations.

691254 – PMID 21067377
691255 – PMID 11781223
691257 – PMID 12764380
691258 – PMID 17377588
691259 – PMID 16642044
691260 – PMID 20625124
691261 – PMID 9864917
691262 – PMID 20668473
691263 – PMID 12850477

Comment entered 2010-12-14 15:39:00 by Kline, Bob (NIH/NCI) [C]

BZDATETIME::2010-12-14 15:39:00
BZCOMMENTOR::Bob Kline
BZCOMMENT::4

I have updated the schema on Mahler to pick up the new attributes you requested. Did the error message really give 'version' with a lowercase 'v'? The DTD has Version (and so do the imported CDR documents). Do you want the Version attribute to be required (as it is in their DTD)? Ready for user testing.

Comment entered 2010-12-14 16:01:06 by Osei-Poku, William (NIH/NCI) [C]

BZDATETIME::2010-12-14 16:01:06
BZCOMMENTOR::William Osei-Poku
BZCOMMENT::5

(In reply to comment #3)
> This appears to be related to items "f" and "g" below.
> It seems the above error message is not the only one. I will see if I can find
> the other error message(s).

Here is the other error message that resulted in importing = 9864917. This one appears to affect item "b" among others.

CDR Advanced Search
Citation added as CDR0000686708 (with validation errors)

      • IMPORTED WITH ERRORS *** PUBLISHABLE VERSION NOT CREATED
        No match found in content model for type Abstract with child elements of Abstract element (AbstractText,AbstractText,AbstractText,AbstractText); stopped at element AbstractText
        Unexpected attribute Label='BACKGROUND AND OBJECTIVE' in element AbstractText
        Unexpected attribute NlmCategory='OBJECTIVE' in element AbstractText
        Unexpected attribute Label='DESIGN AND METHODS' in element AbstractText
        Unexpected attribute NlmCategory='METHODS' in element AbstractText
        Unexpected attribute Label='RESULTS' in element AbstractText
        Unexpected attribute NlmCategory='RESULTS' in element AbstractText
        Unexpected attribute Label='INTERPRETATION AND CONCLUSIONS' in element AbstractText
        Unexpected attribute NlmCategory='CONCLUSIONS' in element AbstractText

Comment entered 2010-12-14 16:04:32 by Osei-Poku, William (NIH/NCI) [C]

BZDATETIME::2010-12-14 16:04:32
BZCOMMENTOR::William Osei-Poku
BZCOMMENT::6

Here is another error that produced by 17377588 which appears to affect item (c).

      • IMPORTED WITH ERRORS *** PUBLISHABLE VERSION NOT CREATED
        No match found in content model for type MedlineCitation with child elements of MedlineCitation element (PMID,DateCreated,DateCompleted,Article,MedlineJournalInfo,ChemicalList,SupplMeshList,CitationSubset,MeshHeadingList); stopped at element SupplMeshList
        Unable to find type for element SupplMeshList

Comment entered 2010-12-14 16:08:09 by Osei-Poku, William (NIH/NCI) [C]

BZDATETIME::2010-12-14 16:08:09
BZCOMMENTOR::William Osei-Poku
BZCOMMENT::7

(In reply to comment #4)
> I have updated the schema on Mahler to pick up the new attributes you
> requested. Did the error message really give 'version' with a lowercase 'v'?

No it was actually an uppercase "V".

> The DTD has Version (and so do the imported CDR documents). Do you want the
> Version attribute to be required (as it is in their DTD)?

No let's not require it.

>Ready for user
> testing.

I have tested this change in Mahler and it looks good. It can be promoted when other changes have been made and tested.

Comment entered 2010-12-14 16:41:26 by Kline, Bob (NIH/NCI) [C]

BZDATETIME::2010-12-14 16:41:26
BZCOMMENTOR::Bob Kline
BZCOMMENT::8

I made the changes needed for the other error messages you reported. Ready for testing on Mahler.

Comment entered 2010-12-14 17:18:26 by Osei-Poku, William (NIH/NCI) [C]

BZDATETIME::2010-12-14 17:18:26
BZCOMMENTOR::William Osei-Poku
BZCOMMENT::9

(In reply to comment #8)
> I made the changes needed for the other error messages you reported. Ready for
> testing on Mahler.

I can't get this CDR0000686708 to validate in Mahler. This is the change in comment #5 (Item b). It looks like the values for the attribute “Label” is set as "BACKGROUND AND OBJECTIVE". If I remember correctly the convention is not to allow spaces between the words?

The other change (comment #6) seems OK and can be promoted when all changes have been tested.

Comment entered 2010-12-15 10:38:41 by Kline, Bob (NIH/NCI) [C]

BZDATETIME::2010-12-15 10:38:41
BZCOMMENTOR::Bob Kline
BZCOMMENT::10

(In reply to comment #9)

> I can't get this CDR0000686708 to validate in Mahler. This is the change in
> comment #5 (Item b). It looks like the values for the attribute “Label” is set
> as "BACKGROUND AND OBJECTIVE". If I remember correctly the convention is not to
> allow spaces between the words?

What you're thinking of is the restriction in DTDs which only allows NMTOKEN values (containing, among other things, no space) in valid value lists, which is the mechanism used by XMetaL to provide a drop-down picklist in the attribute window. If you take a closer look at the error message you're getting, you'll see that the Label attribute's value is not the problem here. The problem is that NLM made another change to the DTD without documenting it. The 2010 DTD allows only a single 'AbstractText' child of an 'Abstract' element. The 2011 DTD allows multiple occurrences of the child element. I have adjusted our schema on Mahler to reflect this undocumented change. Give it another try.

Comment entered 2010-12-15 11:41:22 by Osei-Poku, William (NIH/NCI) [C]

BZDATETIME::2010-12-15 11:41:22
BZCOMMENTOR::William Osei-Poku
BZCOMMENT::11

(In reply to comment #10)
> (In reply to comment #9)
> > I can't get this CDR0000686708 to validate in Mahler. This is the change in
> > comment #5 (Item b). It looks like the values for the attribute “Label” is set
> > as "BACKGROUND AND OBJECTIVE". If I remember correctly the convention is not to
> > allow spaces between the words?
> What you're thinking of is the restriction in DTDs which only allows NMTOKEN
> values (containing, among other things, no space) in valid value lists, which
> is the mechanism used by XMetaL to provide a drop-down picklist in the
> attribute window. If you take a closer look at the error message you're
> getting, you'll see that the Label attribute's value is not the problem here.

OK. Thanks!

> The problem is that NLM made another change to the DTD without documenting it.
> The 2010 DTD allows only a single 'AbstractText' child of an 'Abstract'
> element. The 2011 DTD allows multiple occurrences of the child element. I
> have adjusted our schema on Mahler to reflect this undocumented change. Give
> it another try.

Verified on Mahler. Please promote all the changes to Bach.

Comment entered 2010-12-15 12:38:42 by Kline, Bob (NIH/NCI) [C]

BZDATETIME::2010-12-15 12:38:42
BZCOMMENTOR::Bob Kline
BZCOMMENT::12

Schema modifications promoted to Bach; please check (and close if OK).

Comment entered 2010-12-16 10:08:59 by Osei-Poku, William (NIH/NCI) [C]

BZDATETIME::2010-12-16 10:08:59
BZCOMMENTOR::William Osei-Poku
BZCOMMENT::13

(In reply to comment #12)
> Schema modifications promoted to Bach; please check (and close if OK).

Verified these on Bach. They are all OK.

Another schema change:

CDR 691327 (PMID 19924816) (it looks like this refers to item "e" in comment #1).

Error:

Citation added as CDR0000686712 (with validation errors)

      • IMPORTED WITH ERRORS *** PUBLISHABLE VERSION NOT CREATED
        Unexpected attribute Type='Geographic' in element DescriptorName

Comment entered 2010-12-16 10:46:26 by Kline, Bob (NIH/NCI) [C]

BZDATETIME::2010-12-16 10:46:26
BZCOMMENTOR::Bob Kline
BZCOMMENT::14

Type attribute added to DescriptorName element on Mahler; ready for user testing.

Comment entered 2010-12-16 10:53:55 by Osei-Poku, William (NIH/NCI) [C]

BZDATETIME::2010-12-16 10:53:55
BZCOMMENTOR::William Osei-Poku
BZCOMMENT::15

(In reply to comment #14)
> Type attribute added to DescriptorName element on Mahler; ready for user
> testing.

Verified on Mahler. Please promote to Bach.

Comment entered 2010-12-16 11:04:52 by Kline, Bob (NIH/NCI) [C]

BZDATETIME::2010-12-16 11:04:52
BZCOMMENTOR::Bob Kline
BZCOMMENT::16

Promoted to Bach; please check (and close if OK).

Comment entered 2010-12-16 11:57:44 by Osei-Poku, William (NIH/NCI) [C]

BZDATETIME::2010-12-16 11:57:44
BZCOMMENTOR::William Osei-Poku
BZCOMMENT::17

(In reply to comment #16)
> Promoted to Bach; please check (and close if OK).

This change has been verified on Bach.

Comment entered 2011-01-05 11:22:18 by Osei-Poku, William (NIH/NCI) [C]

BZDATETIME::2011-01-05 11:22:18
BZCOMMENTOR::William Osei-Poku
BZCOMMENT::18

Lowered Priority of this issue to a P7 since we haven't had any more changes for a while. If we don't get any more errors/changes, I will close this issue.

Comment entered 2011-01-18 11:18:07 by Osei-Poku, William (NIH/NCI) [C]

BZDATETIME::2011-01-18 11:18:07
BZCOMMENTOR::William Osei-Poku
BZCOMMENT::19

Closing this issue. We haven't had new failures in about 2 weeks. I will create a new issue if there's a new one.

Attachments
File Name Posted User
Citation changes.doc 2010-11-15 11:06:12 Osei-Poku, William (NIH/NCI) [C]

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