Re: [jats-list] JATS4R draft recommendation for Conflict of Interest statements now open

Subject: Re: [jats-list] JATS4R draft recommendation for Conflict of Interest statements now open
From: "dal dalapeyre@xxxxxxxxxxxxxxxx" <jats-list-service@xxxxxxxxxxxxxxxxxxxxxx>
Date: Fri, 19 Jan 2018 23:01:16 -0000
JATS version 1.1d1 changed the values of @fn-type from a closed list
to an unrestricted (CDATA) list.

Versions of Blue and Pumpkin before 1.1d1 used a closed list.

Debbie


> On Jan 19, 2018, at 5:29 PM, Christina Von Raesfeld tvonraesfeld@xxxxxxxx
<jats-list-service@xxxxxxxxxxxxxxxxxxxxxx> wrote:
>
> Hi Charles,
>
> You indicated below that "the model for fn-type is CDATA, so both "conflict"
and "COI-statement" would be valid in JATS 1.1 (blue)".
>
> Wanted to chime in that in the Blue DTD, it appears overrides are defined in
JATS-journalpubcustom-models1.ent that restrict fn-type to the enumerated
list.
>
> Using @fn-type="COI-statement" in JATS 1.1 (blue) produces this error:
>
> Schema: http://jats.nlm.nih.gov/publishing/1.1/JATS-journalpublishing1.dtd
> Engine name: Xerces
> Severity: error
> Description: Attribute "fn-type" with value "COI-statement" must have a
value from the list "abbr com con conflict corresp current-aff deceased
edited-by equal financial-disclosure on-leave participating-researchers
presented-at presented-by present-address previously-at study-group-members
supplementary-material supported-by other ".
>
> Cheers,
> Tina von Raesfeld
>
> PLOS I OPEN FOR DISCOVERY
> Tina von Raesfeld I Production Technical Lead
> 1160 Battery Street, Suite 225, San Francisco, CA 94111
> tvonraesfeld@xxxxxxxx I Main +1 415-624-1200 I Direct +1 530-588-2603 I Fax
+1 415-546-4090
> plos.org I Facebook I Twitter I Blog
>
>
> From: Charles O'Connor coconnor@xxxxxxxxxxxx
<jats-list-service@xxxxxxxxxxxxxxxxxxxxxx>
> Sent: Thursday, January 18, 2018 8:43 AM
> To: jats-list@xxxxxxxxxxxxxxxxxxxxxx
> Subject: Re: [jats-list] JATS4R draft recommendation for Conflict of
Interest statements now open
>
> There was a discussion of this topic on the Google doc while it was open.
This is the last thread I have. I don't know how or whether it was resolved
(see below).
>
>
>
> Two clarifications about comments in this thread: 1) the model for fn-type
is CDATA, so both "conflict" and "COI-statement" would be valid in JATS 1.1
(blue). 2) The PMC recommendation for JATS 1.1 is to use "conflict" in Blue
and "COI-statement" in Green. I have no information on the reasoning behind
the difference.
https://www.ncbi.nlm.nih.gov/pmc/pmcdoc/tagging-guidelines/article/tags.html#
el-fn
>
>
>
> -Charles (AKA Joebob Jones)
>
>
>
>
*****************************************************************************
***************************************************************
>
>
>
> Christina Von Raesfeld replied to a comment on Conflict of Interest
Statements - Draft Recommendation.docx
>
> ________________________________________________________________
>
> Joebob Jones
>
> statement
>
> Why "COI-statement" as the value? The JATS tag library recommends "conflict"
for conflict of interest statements, and I know many publishers use
"conflict". Are there also many who currently use "COI-statement"? If not,
then this would create a split with much legacy XML that would otherwise
already conform to this recommendation.
>
> ________________________________________________________________
>
>  Luciano Panepucci
>
> I agree. We have been using "conflict" as suggested in JATS[1].
>
>
>
> I just checked the PMC tagging guidelines and to my surprise it specifies
"COI-statement"[2]. I wander when was this changed or was it always like this?
(couldn't find in the update history)
>
>
>
> [1]
https://jats.nlm.nih.gov/publishing/tag-library/1.1/attribute/fn-type.html
>
>
>
> [2]
https://www.ncbi.nlm.nih.gov/pmc/pmcdoc/tagging-guidelines/article/tags.html#
el-aunotes
>
>
>
> ________________________________________________________________
>
> Christina Von Raesfeld
>
> @fn-type="COI-statement" is invalid in the JATS Journal Publishing (Blue)
DTD. We use @fn-type="conflict", and PMC does dictate @fn-type="conflict" for
the Blue DTD:
>
>
>
>
https://www.ncbi.nlm.nih.gov/pmc/pmcdoc/tagging-guidelines/article/dobs.html#
dob-coi
>
>
>
> "For a COI statement captured as <fn> in the Journal Publishing (Blue) DTD,
use @fn-type="conflict". Otherwise, use the appropriate content type attribute
with a value "COI-statement"."
>
>
>
> Also, we do not include the "Competing interests:" label in the footnote and
instead rely on both our and PMC's software to render a "Competing Interests:"
label in front of all @fn-type="conflict" footnotes. If you include the label
in the fn/p, as shown in the JATS4R examples, then it will result in a double
label in the PMC rendering.
>
>
>
>
*****************************************************************************
*****************************************************************
>
> -----Original Message-----
>
> From: Alf Eaton eaton.alf@xxxxxxxxx
[mailto:jats-list-service@xxxxxxxxxxxxxxxxxxxxxx]
>
> Sent: Tuesday, January 16, 2018 5:50 AM
>
> To: jats-list@xxxxxxxxxxxxxxxxxxxxxx
>
> Subject: Re: [jats-list] JATS4R draft recommendation for Conflict of
Interest statements now open
>
>
>
> On 7 December 2017 at 18:24, Kelly McDougall kmcdouga@xxxxxxx
<jats-list-service@xxxxxxxxxxxxxxxxxxxxxx> wrote:
>
> >
>
> > Hello JATS users,
>
> >
>
> > JATS4R working group has developed a draft recommendation for the tagging
of Disclosure of Conflicts of Interest/Competing Interest statements. This
recommendation is open for comment. Please make comments on  the google doc
version
<https://docs.google.com/document/d/1tJltI28KpqUqI5_c2RH5470RnTdb63yaMYQ6_Moh
qDU/edit?usp=sharing>, which is publicly available. The deadline for adding
comments is Friday, January 5th, 2018.
>
> >
>
> >
>
> > All the best,
>
> >
>
> > Kelly McDougall
>
> >
>
> > JATS4R Standing Committee
>
>
>
>
>
> If it's not too late (the doc no longer allows comments, so it may be, but I
only just saw this note), I'd like to point out that the JATS documentation
already includes an example of marking up "conflicts of interest" statements
with `fn-type="conflict"`:
>
> https://jats.nlm.nih.gov/publishing/tag-library/1.1d1/n-hxx0.html
>
>
>
> This can be used in article XML as follows:
>
>
>
> <fn-group content-type="competing-interests">
>
>     <title>Competing Interests</title>
>
>     <fn id="conflict-1" fn-type="conflict">
>
>         <p>The authors declare there are no competing interests.</p>
>
>     </fn>
>
> </fn-group>
>
>
>
> e.g. https://peerj.com/articles/3000.xml
>
>
>
> Alf
>
>
> JATS-List info and archive
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Deborah A Lapeyre              mailto:dalapeyre@xxxxxxxxxxxxxxxx
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