Re: FW: [jats-list] Element for wrapping a group of xref e

Alf,

My experience has been that some downstream XML consumers do complain about use of multiple RIDs. So you need to check with the consumers of your XML before heading in this direction to see if it's a problem for them. Of course you can always use multiple RIDs in your master XML in-house and XSLT your way to an alternate form for delivery to any consumer who has problems with this structure.

Best regards,

Bruce

At 10:23 AM 1/24/2013, Alf Eaton wrote:

That's correct, there isn't an issue with the JATS DTD in this case.
However, I believe that this list is also for users to discuss best
practices when creating or consuming XML that conforms to the JATS
DTD.
In particular, I'm looking for feedback on whether attempting to store
the context of all citations (by making sure they're all noted in the
xref @rid) is worth the possible complications of downstream consumers
not expecting multiple rids, and whether any best-practice precedents
have been established elsewhere (i.e. is anyone else doing this, and
have they encountered any problems).
Apologies if it's not directly schema-related, but there doesn't seem
to be a more appropriate place for this discussion :-)
Alf

On 24 January 2013 14:43, Randall, Laura (NIH/NLM/NCBI) [E] <laura.randall@xxxxxxx> wrote: > Alf, > As has been pointed out before, the Tag Suite does, in fact, allow you to include space-separated values in @rid. > > What you're describing is an issue with PMC, not with the JATS. If you're concerned about the content display in PMC, please contact them directly at pmc@xxxxxxxxxxxxxxxxx > > Thank you, > Laura > ________________________________________ > From: Randall, Laura (NIH/NLM/NCBI) [E] > Sent: Thursday, January 24, 2013 9:37 AM > To: jats-list@xxxxxxxxxxxxxxxxxxxxxx > Subject: RE: FW: [jats-list] Element for wrapping a group of xref elements > > Alf, > As has been pointed out before, the Tag Suite does, in fact, allow you to include space-separated values in @rid. > > What you're describing is an issue with PMC, not with the JATS. If you're concerned about the content display in PMC, please contact them directly at pmc@xxxxxxxxxxxxxxxxx > > Thank you, > Laura > ________________________________________ > From: Alf Eaton [eaton.alf@xxxxxxxxx] > Sent: Wednesday, January 23, 2013 11:47 AM > To: jats-list@xxxxxxxxxxxxxxxxxxxxxx > Subject: Re: FW: [jats-list] Element for wrapping a group of xref elements > > Another example where multiple, space-separated "rid" attributes in an > <xref> would be beneficial is when a numeric range is used as the > citation label: <xref ref-type="bibr" rid="ref-12 ref-13 ref-14 > ref-15">12-15</xref>. > > At the moment there are articles in PMC where the context for some > citations is missing, as the articles are marked up <xref > ref-type="bibr" rid="ref-12">12<xref>-<xref ref-type="bibr" > rid="ref-15">15</xref> - there's no context for the citation of > references 13 and 14. Luckily there's no data loss as the range can > still be interpreted as "references 12-15", but it does mean that some > references don't display in the PMC sidebar when a numeric range is > cited. > > On 9 January 2013 14:19, Alf Eaton <eaton.alf@xxxxxxxxx> wrote: >> Thanks Jeff. I was thinking that in places where a single xref links >> to multiple target ids, a list of the targets could be displayed and >> the user can choose which one they want (this would work for >> references, tables or figures). The default - for when Javascript is >> disabled - could be to link just to the first of the targets. >> >> I haven't tried that yet to see how well it will work in practise, though. >> >> On 9 January 2013 12:52, Beck, Jeff (NIH/NLM/NCBI) [E] >> <beck@xxxxxxxxxxxxxxxx> wrote: >>> Hi Alf, >>> >>> PMC can handle multiple values in xref/@rid. We do have issues generating >>> the display if the xref is empty (but we have that for single values, >>> too), and of course the links are problematic. >>> >>> <xref ref-type="fig" rid="d349665qxx"/> or <xref ref-type="fig" >>> rid="d349665qxx d34888324qqq"/> are both tough to figure out what to do >>> with. >>> >>> <xref ref-type="fig" rid="d349665qxx d34888324qqq">Figs. 1 & 2</xref> >>> is not a problem unless you want "1" to link one place and "2" to link to >>> another - which is generally what users expect. >>> >>> I'd prefer >>> >>> Figs. <xref ref-type="fig" rid="d349665qxx">1</xref> & <xref >>> ref-type="fig" rid="d34888324qqq">2</xref> >>> >>> Or even >>> >>> <xref ref-type="fig" rid="d349665qxx">Figs. 1</xref><xref ref-type="fig" >>> rid="d34888324qqq">& 2</xref> >>> >>> >>> Remember, the PMC Tagging Guidelines are just that - guidelines. PMC >>> requires content that is well-formed, is valid to the schema it claims to >>> follow, and represents the article(s) and publication model of the journal >>> accurately. >>> >>> Questions on PMC can be addressed to pmc@xxxxxxxxxxxxxxxxx >>> >>> Jeff >>> >>> >>> >>> >>> >>> On 1/8/13 5:40 PM, "Alf Eaton" <eaton.alf@xxxxxxxxx> wrote: >>> >>>>Jeff, would you be able to comment on whether this actually is a >>>>restriction of PubMed Central? It seems like it would be nice to mark >>>>up a collection of references as one element, but I guess it's >>>>forbidden by PubMed Central because the HTML display can't handle it? >>>> >>>>I could work around the restriction by adding another element around >>>>the whole group of references, perhaps, though I'm not sure what >>>>element that would be. >>>> >>>>Alf >>>> >>>> >>>>---------- Forwarded message ---------- >>>>From: Alexander Schwarzman <aschwarzman@xxxxxxxxx> >>>>Date: 5 December 2012 18:57 >>>>Subject: Re: [jats-list] Element for wrapping a group of xref elements >>>>To: jats-list@xxxxxxxxxxxxxxxxxxxxxx >>>> >>>> >>>>I think one has to consider whether the articles are going to be >>>>submitted to PubMedCentral. >>>> >>>>PMC Guidelines >>>>http://www.ncbi.nlm.nih.gov/pmc/pmcdoc/tagging-guidelines/articl e/tags.htm >>>>l#el-xref >>>>admonish: >>>> >>>>Do not tag multiple id values in @rid. >>>> >>>>--Sasha >>>> >>>>On Wed, Dec 5, 2012 at 8:36 AM, Bruce Rosenblum <bruce@xxxxxxxxx> wrote: >>>>> Alf, >>>>> >>>>> You can tag in all versions of NLM or in JATS as: >>>>> >>>>> "induce co-stimulatory molecule elevation<xref rid="r14 r15 >>>>>r18">14, >>>>> 15, 18</xref>" >>>>> >>>>> This works fine for references, and you can also do the same with >>>>>tables or >>>>> figures, as in: >>>>> >>>>> <xref rid="t1 t2 t3 t4">Tables 1-4</xref> >>>>> >>>>> but beware that this may create a usability problem for the reader >>>>>because >>>>> there's no "point" on which you can click to go to table 2 or table 3. >>>>>This >>>>> is less of a problem with references since they are all in the same >>>>> proximity. >>>>> >>>>> In both cases, the key behind this is that the DTD declares rid to be >>>>> IDREFS, not simply IDREF. >>>>> >>>>> Bruce >>>>> >>>>> At 08:26 AM 12/5/2012, Alf Eaton wrote: >>>>>> >>>>>> Is there an element in the JATS DTD that is suitable for denoting a >>>>>> collection of xref elements in the body of an article? >>>>>> >>>>>> For example, in various citation styles: >>>>>> >>>>>> "induce co-stimulatory molecule >>>>>> >>>>>> >>>>>>elevation<xref-group><xref>14</xref>,<xref>15</xref>,<xref>18< /xref></xr >>>>>>ef-group>." >>>>>> >>>>>> "induce co-stimulatory molecules elevation >>>>>> <xref-group>(<xref>Gagliardi 2000</xref>; <xref>Berin >>>>>> 2008</xref>)</xref-group>." >>>>>> >>>>>> "induce co-stimulatory molecule >>>>>> elevation<xref-group>[<xref>14</xref>-<xref>16</xref>]</xref-group>." >>>>>> >>>>>> If the citations were marked up in this way, then it would be possible >>>>>> for the renderer to choose which style >>>>>> (numeric/superscript/parenthetical) to use when rendering them. >>>>>> >>>>>> For example, <xref-group><xref rid="ref-14">14</xref><xref >>>>>> rid="ref-15">15</xref><xref rid="ref-16">16</xref></xref-group> could >>>>>> be turned into a comma-separated list of numbers, a hyphenated pair of >>>>>> numbers, or a semi-colon-separated list of author/year pairs, with the >>>>>> appropriate punctuation. >>>>>> >>>>>> Thanks, >>>>>> Alf >>>>> >>>>> >>>>> ------------------------------------------------------------------- >>>>> This email message and any attachments are confidential. If you are not >>>>>the >>>>> intended recipient, please immediately reply to the sender or call >>>>> 617-932-1932 and delete the message from your email system. Thank you. >>>>> ------------------------------------------------------------------- >>>>> Bruce D. Rosenblum >>>>> Inera Inc. >>>>> 19 Flett Road >>>>> Belmont, MA 02478 >>>>> 617-932-1932 (office) >>>>> bruce@xxxxxxxxx

------------------------------------------------------------------- This email message and any attachments are confidential. If you are not the intended recipient, please immediately reply to the sender or call 617-932-1932 and delete the message from your email system. Thank you. ------------------------------------------------------------------- Bruce D. Rosenblum Inera Inc. 19 Flett Road Belmont, MA 02478 617-932-1932 (office) bruce@xxxxxxxxx

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