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: "Christina Von Raesfeld tvonraesfeld@xxxxxxxx" <jats-list-service@xxxxxxxxxxxxxxxxxxxxxx>
Date: Fri, 19 Jan 2018 23:54:05 -0000
Ah, thanks. With that in mind, even in the v1.2d1 Tag Library documentation
(all colors), I see that "conflict" remains the suggested value for Conflict
of Interest statements ("COI-statement" is not listed at all), so even though
it will be an unrestricted list for all publishers using v1.2d1 and later, it
still seems like JATS4R should be endorsing the value that is and has always
been the tag library's suggested value, not "COI-statement". If PMC has been
dictating "conflict" for Blue users, but "COI-statement" for non-Blue users,
it sounds like what should change is that PMC should lift their
"COI-statement" requirement for non-Blue users so those publishers can begin
honoring the tag library's suggested value without having to transform the
value for PMC.


Tina


________________________________
From: Tommie Usdin btusdin@xxxxxxxxxxxxxxxx
<jats-list-service@xxxxxxxxxxxxxxxxxxxxxx>
Sent: Friday, January 19, 2018 2:39 PM
To: jats-list@xxxxxxxxxxxxxxxxxxxxxx
Subject: Re: [jats-list] JATS4R draft recommendation for Conflict of Interest
statements now open

In JATS 1.2d1 (that is, the first draft of what will probably become JATS
1.2), the model of @fn-type is unconstrained. See:
https://jats.nlm.nih.gov/publishing/tag-library/1.2d1/attribute/fn-type.html

Attribute: Type of Footnote -
jats.nlm.nih.gov<https://jats.nlm.nih.gov/publishing/tag-library/1.2d1/attrib
ute/fn-type.html>
jats.nlm.nih.gov
hide the sidebar + ; How To Use (Read Me First) Root Element; General
Introduction; Selecting a Model & Schema




While it is possible that this draft will change, and that that the value of
@fn-type will remain constrained in JATS 1.2, it seems unlikely.

 Tommie


> 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

jats.nlm.nih.gov<http://jats.nlm.nih.gov/publishing/1.1/JATS-journalpublishin
g1.dtd>
jats.nlm.nih.gov
%journalpubcustom-modules.ent; %modules.ent; %JATS-ali-namespace.ent;
%JATS-common-atts.ent; ...



> 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

PubMed Central Tagging Guidelines
[article]<https://www.ncbi.nlm.nih.gov/pmc/pmcdoc/tagging-guidelines/article/
tags.html#el-fn>
www.ncbi.nlm.nih.gov
Elements. These XML elements have specific style rules associated with them.
This is not a complete list of XML elements included in the tag set.



>
>
>
> -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

Attribute: Type of Footnote -
jats.nlm.nih.gov<https://jats.nlm.nih.gov/publishing/tag-library/1.1/attribut
e/fn-type.html>
jats.nlm.nih.gov
There are many reasons why the text or metadata of an article might be
footnoted. Where those reasons are known (for example, the reasons are listed
in the suggested ...



>
>
>
> [2]
https://www.ncbi.nlm.nih.gov/pmc/pmcdoc/tagging-guidelines/article/tags.html#
el-aunotes

PubMed Central Tagging Guidelines
[article]<https://www.ncbi.nlm.nih.gov/pmc/pmcdoc/tagging-guidelines/article/
tags.html#el-aunotes>
www.ncbi.nlm.nih.gov
Elements. These XML elements have specific style rules associated with them.
This is not a complete list of XML elements included in the tag set.



>
>
>
> ________________________________________________________________
>
> 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

PubMed Central Tagging Guidelines
[article]<https://www.ncbi.nlm.nih.gov/pmc/pmcdoc/tagging-guidelines/article/
dobs.html#dob-coi>
www.ncbi.nlm.nih.gov
Where multiple formats (gif image, text, jpg image) of a single object
(figure, table) are available, specify @alternate-form-of on all non-primary
...



>
>
>
> "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
>
>
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