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Extending JATS to include the NISO/NFAIS Recommended Practices for Online Supplemental Journal Article Materials

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OK today are going to be presenting an exact extension to support nice recommended practices for online support supplemental journal article material so this presentation will
review nicest 2013
recommended practices for online Supplemental Generic materials which is a lot to say so I'll refer to it as the nice so API moving forward I will cover the extension of the created jets will talk about some of the constraints to use during the modeling process and show you a schematic of the extension and then the final portion of the presentation will be a discussion on the these theoretical issues that we encountered while working on extension so all yesterday about how
publishers work with supplementary materials may still in anything and put together a working group to identify and address some of the issues that came up and in early 2013 the Committee published a set of recommended practices which provided recommendations on metadata needed to manage supplemental materials throughout the life cycle and they provided us with some required and optional metadata which we did take into account when we're working on extension and then they also provided 1 potential expressions of the nice API through non-normative DTD which we want to consider the following exactly instead we took the recommended practices and the non-normative DTD together to understand the importance the structures that sparse so although a large number of
elements and actually it's defined in the non-normative DTD the nasality defined actually relatively few of these as required they're actually 7 required elements and 1 required actually is and they cover those required of that required metadata theorem so you schematic to come and lay the groundwork to help you understand what we did with the expansion so the 1st required element we have this article metadata and this is a container for metadata concerning the article to which materials are supplemental article identifier is a persistent public identifier of the article by best practice DOI supplemental material descriptive metadata this is a container for descriptive metadata of supplementary materials such as title caption labels history and preservation supplemental material identifier this is a persistent public identifier of the supplemental material then
we have supplemental material object metadata container for descriptive and physical metadata used to describe 1 supplemental material object supplemental material physical metadata this is a container for physical information of supplemental information such as file format size mime type in mind subtypes and then last we have format which is the format of the file containing the supplemental material and then we have our 1 required at tribute which is supplemental material type which can hold the value of additional England or integral 5 additional supplemental materials include objects that provide additional relevant and useful extension of the article that you not form part of the intellectual work whereas interval supplemental materials include objects considered a necessary part of the intellectual work there also several optional
elements and attributes and that kind of bring up that depth of description and is going point out 2 of them on this list here and 1 of the Supplemental Material label and that's how the object is referred to directly from the text of the article and then supplemental material contributors allows for identification of the creators of or contributors to the supplemental materials and you can see a list of the here presentations so this is a schematic
representation of the non-normal DTD you can see at the very top here we have the right elements the 2nd metadata and then below that all we have article metadata so any type of the associated metadata would be like a wrapper of this section in an article metadata would be information about the article to which these are supplemental we have some that descriptive inconsistent descriptive information and then the main object there element to look at here so that object metadata and in this case we call this the media PDF I mean I haven't actually done it that type so this is additional material and that he had never descriptive and physical information and then we see that some that object metadata recurse underneath that for a final berth figure with not PDF file and in that have article article component metadata which tells you where it was described in article and descriptive information and and once again we see some that object metadata recursing off another figure within the PDF file the so after we
are understood the next so artfully and non-normative dt is best could be decided to create some constraints for the modeling process and in nicer Lockheed tax samples provided with the supporting documentation were delivered as stand-alone documents it is possible that other applications might choose to keep this information in a separate file that we have bringing this into the fold of jacks and decided that information about supplemental materials should reside in the same XML document that describes article for which they are part so the supplementary material will be from inside Jets article so for this reason to have the required elements in ISO API article metadata in article identifier and we actually set those aside because this information encode is already covered by the elements found in articles front element and Jack and then the upper level of the RIP if you remember that such that metadata that red element of the set that aside because it was used as a route from and supplementary material was a stand-alone document and the function of wrapping the supplementary material section together can be found in jackson using the fact elements so last 2nd
constraints and we decided that any place where Jackson I sloppy or the non-normative DTD have common elements in that they express the same concept we would take from Jack rather than the model on more than 1 norm the for the non-normative DTD such as and we use the Jets controversy history and actually mind type and over the suggestions in the non-normative dt when there was no corresponding jets concept and we use the elements and attributes from the non-normative DTD and for the sake of clarity we put them in a namespace and which we call the X T for extension sample can be of this can be found in a constraint number 3 so what are
constraints and we decided we would change the descriptive names if we felt that it either made more sense or led to better alignment with Jack and the next 2 elements provenance and preservation were taken as they are because there's no now this structure some of these in Jack's however we did change the names to EXT over regional sources and NEXT preservation level so the truth
to emerge from a sloppy with Jax we had to think about how structure it and we can so that we could fit into death problem can just drop it in the job because there would be a mismatch in structures we we really had to think about how to reconcile the 2 and as previously discussed we are in the 1st bullet point we use the death elements acting in place at the top level my so elements that metadata and and then also we felt that the price level at which that sort max object metadata about recursive elements that was being used was equivalent to the jack supplementary material and as we look for the reader determined that object supplementary material model contains much that not all the the content found under certain that object metadata so we would need to add content to the jack supplementary material model some of this would be entirely new to Jack and that other constant existed within the Jets model from although it was not found inside supplementary material and then also when were trying to use the nice non-normative DTD and to understand how the knife API can be used in practice and 1 difficulty we have was that we would find ourselves and getting lost in the recursive structure of the text samples even as we were looking at the publisher version of the supplementary material and this led us to believe that it might be helpful for orientation if their word distinctions to be made as you walked down the levels inside a particular piece of supplementary data In particular some levels had physical information associated with them such as file size and file format while when you reach the level of describing a discrete piece of a single file such as an individual figure with an appeal last and this physical information behind that so we decided it might be more intuitive to use 2 different elements I want to describe objects that have a physical presence in that they can be addressed within the file system and we call this element resources and 1 to describe objects that can also be referred to in that are logical parts of individual file we call that the existing item so in using EXE resource EXE item even deprecated that recursive elements from an ISO are piece of matter object metadata OK so this is and what
the comparison of the 2 so you can understand the structure so that again with a file that has several PDFs within it and then the next level is the level of maybe 1 of those PDFs and and then that got the lowest level is a figure within individual pdf so here are some we have that wrapper elements that not metadata at the highest level and authority and then we have found that some Mac object metadata for that in particular for that file can have descriptive and physical information and then you see this recurs for the individual PDF even for the figure within the PDF and for the extension we have just that the supplement the supplemental material from section and then we have the supplementary materials hand that can have label captions and because the file with the pdfs and it has some physical information we have been we use the Xt resource out and then at the level of actually and there's also a physical information see that the existing resource recursing again and then at the level of that individual figure then we have an item because there's descriptive information available so some other considerations and
that we made after making changes to the jet supplementary material model we decided to look back and see were also changes might be helpful and we decided to make some changes to the Japs element Fig of which came from 2 different areas we've been thinking about it essentially the same time in the 1st was to include a new structures EXT resources the EXT items interface and because we like the areas of content at the nice working group had included in their description of supplementary material which we then had incorporated into Ressourcen item and we thought that it offered richer description because it allows for explicitely labeling information related to preservation and separate authorship history of the object and it is thought this would be helpful are more useful for discovering non supplementary materials as well so the ultimate EXT resource in this place is not going to take on the place of graphic and media and then the 2nd 1 is that we have specifically addressed 1 of the required parts of the NI key and it would be whether that we were stating an object being described is considered an integral and or additional to the article in the API of nice lucky if you remember that time interval additional value is held on activated but not object metadata and the course remember we started deprecate suddenly object metadata so we made the assumption for our extension that would be nice refers to add additional materials could be marked up with the supplementary material model which would leave elements like they have to use to use to mark up integral materials and this that well within our decision to make the models for supplementary materials and face the same so here we
have a schematic of supplementary material section in an article that we shorten down to the word way out I am in so here's the supplemental information section in that you see we have a a document s 1 a PDF conduct 1 has to figures Table S 2 supplemental experimental procedures and acknowledgments within it and then you see an excel file and which is document X S 2 that has to have 1 in next we haven't audio file s 1 and then we also have audio file as to so here's a schematic what that might look like and using the extension so 1st we're gonna
start with the section called supplementary material and then I want to work with that 1st pdfs and that document s 1 so it has a label and has the caption title and then they have some physical information the PDF does so we have resources and then there are remember there's on several things wasn't with inside this there are 2 figures in the table and a bunch of other things and so if we do it that 1st Figure S 1 we're going to use the item and it has the label the captain in the title of a descriptive information with and then the column can recurse under that to describe the other figure in all of the other things that are inside that dbpedia but also within that
supplementary material and information
section of this article was this Excel file which removed for brevity here and and then the
next thing I this was the audio file audio US 1 so here it is and so we have
another supplementary material tag here of the descriptive information and then the physical information is under resource on energy can see there's no item-level here because there there was no descriptive information about lower level for but in the obvious to we also removed for brevity we have another
example of using something called redox but
also gives you that I am in if you would like to see
later you can otherwise all of supporting documentation is available at this link the DTD files for the extension of their documentation for the extension and examples of the nicest samples that we marked up using the extension there's where so you it might appear that we should have
another bullet point on this slide which is something about 0 now please go
look at our implementation of this extension and please use this because it's wonderful and it's going to solve all your problems but there is no such bullet point in there will not be an Bruce on I apologize to you I think you were hoping we had at point in the
set of proper it seemed like you had hoped for that and when you mentioned I talk the other day but the polar point doesn't exist and that there's a reason that it
doesn't exist but I will read this very slow
it just not quite we want what
else we were using the extension we found tensions in it on AI
and I'm not going to go through like an amazing laundry list of different problems we found as we try to use and understand make 2 main points the 1st
is as Karen mentioned we had restructured subnet object medal into 2 additional elements to take its place 1 being resource the other being I down because we thought this was going to help us keep track of information in a slightly better way and it actually didn't I don't think it made anything worse but it didn't really believe are confusion on particularly when you have complex supplementary data objects a single objects maybe you know a single PDF that you were not pulling out additional pieces of information in a single excel file we didn't have any trouble with but if the examples that more and more complex
we would find if Karen and I looked at it separately we would come up with 2 different ways to tag it than when we sat down together chat about it we might come up with a 3rd way to tag and that makes you a little suspicious but the 2nd thing is that we sense the whole
DTD package whole extension package to mother technologies for an idea and the this is an independent validation and verification maybe verification validation of forget which 1 on and what they do is they'll check the entire package out from can I just take it drop it in what I need to will it work you know will work at
x parser and persons he pass a will work on this platform that platform but additionally there will look at the DTD itself and what they feel about it so we pass the technical stuff rather decently so if you guys do you
want to go and try to to use this you should have a technical barrier in trying to use on on
the other hand and this that goes with that 1st point we made on the slide is there was a concern expressed we were doing some mingling of content and metadata in a way that they didn't like some which and so on that would be an amazingly right topic for conversation either afterward and not all would be an entirely different people on there's that that's probably that much meat in talking about this but I'm just leave it at that and say the user to the reasons they give you an idea of why we were all that happy with the
extension and why were not so jumping up and down Tony all the users of at the same time we're having all these issues time use the extension I get an analogy stuck in my head which I'm now going to inflict upon all of you which is
that we had sort of created the creature from Frankenstein from Mary Shelley's Frankenstein in particular in that we have
taken these pick these bits and pieces from things they're perfectly usable on around nothing wrong with jets and this is having nothing really desperately wrong with the nicer Lockheed but yet when we picked and choose to put it together and added a little of our own flavor to it we want up with something I will not call a grotesque grotesque is which quoted on the slide but it really was unwieldy and I know this is a really touchy feely thing that I it's hard to describe but it's 1 is in an elegant it is it works but it's gonna take tension and friction to use it properly and to get anything out of it I think on nothing you couldn't power through it and use its expressive enough I believe but I yet more handwaving more so
you know we see we step back a little bit and then say well why not because we really thought this would be this if not simple to do simple conceptually to do because Jackson's jets it's used in the community the nicer Lockheed you know look at it by itself it seems pretty reasonable the obvious thing to do was to try to put these 2 things together yeah more handwaving so it's hard to say it just it just it didn't work for us for whatever reason and here we wondered whether it was because chapter you know it's time to reflect current practice whereas the nice a lot he's trying to manage a little bit it maybe those 2 things don't go together and might in a small part of what was going on but I don't think it explains you have the entire problem on and after a lot of certain back and forth and talking amongst ourselves and talking with some other people what we came to believe that exceeds the was the major problem was was actually supplementary material was
it's just this concept we understand we all understand it we all understand how it's evolved yet we think this is what's
causing the trouble in the model models the fact that things that otherwise we would know how does she handle without without blinking the figure that out there at the table that's out there yet we've label that supplementary 1st and therefore it's gotten tossed in a bucket and it's really easy show the smoking sign in and now not want to deal with it in the way that we would normally deal with this if it was part of the article proper so in order to have a nice and excuse me a nice catch phrase of we think we have pointed this term if anybody else is used to before apologies but we think 1 of the major problems is that there is a single we'll call supplementary material exceptional was that as soon as something becomes supplementary we treated differently now on the other hand we understand why this has happened we understand that you know nobody is going to go change their models this is deep in business models CSG with the transition from print to electronic it has to do with the fact that another yeah there are electronic versions of journals people want to add more and more and more because they don't really see a reason not to there's not the page limit yet this is all this together is creating this tension and on we say think maybe ending
supplementary material exceptionalism might Help the the modeling problem now this should be taken more as a thought experiment than anything else this is not I'm not at all advocating that you all run out and get rid of your supplementary material or start taking it entirely differently too many barriers but I think there's there's thinking about for just a little while
of this the and so if we can if we want to get rid of supplementary material exceptionalism in a way we have to get rid of supplementary material and 1 way we thought of doing this is you know this year when Chairman not 1 turn was talking previously once we had started change the supplementary material modeling jets to take on some of the nice so information we also then went back and changed figure to also take some of that information into account because we thought that richer model was pretty interesting so it seems to lead to In apologies I when I listened to Tommy's talk yesterday I thought 0 my gosh she's going cringe generics and
again a thought experiment there be many ways to potentially deal with this problem 1 of the ways we thought of was the potential use of generics a I'll just read the this 1st thing and I don't think I've got the definition right that's why there are parentheses and a question mark in the 1st point but maybe you know we need a generic that holds block-level elements that are allowed to float but don't reference external files directly so that type of thing and thinking about our figure table wrapped supplementary material on world the definition should be such that we exclude graphic and media were not trying to lump graphic and media into this generic we 1 want them into a different genera on and you know as we talked to some people you notice that I welcome you do that 1 not resist why not append X
and I'm not sure I mean I don't that proposes is that true workable solution we did not do that the 2nd point would be at as a 2nd generic
on which incorporates graphical media into a single element not the same thing more about that a and the 3rd thing you would need since we're talking about an ISO Lockheed supplemented it's still need to know to somehow what is supplementary and what is not supplementary alongside retirement and I stop maybe that's just binary distinction between interval an additional but I think you could actually imagine a richer world where you might see on he has a lot more maybe there's of either as large transition between things that are absolutely necessary things that are we off there might be a sliding scale you might say 0 this is interval if you are going to attempt to repeat the experiment you need to see this piece of material but if you're not that interesting repeating the
experiment you know it's additional to and just to other points to make about this 1 is that you'll notice we did try to give these generics names because I think if we try to name it would all be
about the mean and not the concept and the 2nd thing is that and it's you partially because again when it was an interesting 1 time he was talking about this yesterday you often generic so because people think tanks is to be the trend make it smaller that's exactly why I brought generics into this I think graduates into it because In the world
of taxonomy and cataloging and things like that the lumpers and the splitters and I think a bit of a lumper and I see a lot of these things is being on the on the outside similar so they could be in a generic and you can then start typing inside you know doesn't have to be much of a loss ' semantics just because you don't use figure or table ramps that can be attached somehow unattributed and
on where this school where were we in school or college or something cover the last line on that slide would just be the imperative sentence discussed period and exercise and going yeah I'm I'm not going to create any more discussion on this is just a potential thing to
think about intercom discussion so action that
it's upon are wrapped up is that you know we did do this extension of although we don't much like the results it is up and it is available for people to try to use on me it's possible I think it could be possible either way somebody else might pick it up and think it's not as horrible as we think it happens on somebody might be able to pick it up and say 0 it's just this 1 thing that you did wrong maybe yeah that's what I make this 1 change in DTD and all is well I'm not too sure about we're happy
for people to look at it on we also take
a certain point of pride when we got there the IV and V from Mulberry included the sentence an experiment that points out this many problems is by definition success so that was our take home 20 and I and we will hold their clothes and something that we like and the 2nd thing we did was proposed that on why this was as hard as it was was because of this idea we've we've come to think of the supplementary material exceptionalism a-and and maybe the community just needs to think about it I I don't actually know that this would solve all of our problems that maybe it would help a little bit on just as a final
fate you just mentioned the bad
of curing did this work while she was part of that she still is produces its Fellows program but she was on campus of last year so we'd like to thank the program she was here project certainly would not have gone done but just back to where the proposal this would not abandon proposal has not been written and of course just has exceedingly deep knowledge of the jet tedium is very useful and also helped us a lot with the technical creation of the DTD and finally on I hope he is not embarrassed I would like to point out such a sportsman we had a number of very good discussions with him starting with the lunch hour during the summer and offer better or worse that lunch I think spond us in the direction of supplementary material exceptionalism so that would be all thank you
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Metadaten

Formale Metadaten

Titel Extending JATS to include the NISO/NFAIS Recommended Practices for Online Supplemental Journal Article Materials
Serientitel JATS-Con 2013
Teil 11
Anzahl der Teile 16
Autor Gutzman, Karen
Tryka, Kimberly A.
Lizenz CC-Namensnennung 3.0 Unported:
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DOI 10.5446/21793
Herausgeber River Valley TV
Erscheinungsjahr 2016
Sprache Englisch
Produktionsort Washington, D.C.

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Dauer 30:02

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Fachgebiet Informatik
Abstract This paper discusses our experience of creating an extension for JATS that incorporates the NISO "Recommended Practices for Online Supplemental Journal Article Materials" (NISO RP-2013). We will discuss our analysis of the recommendations and our comparison of the recommendations with JATS, as well as our thrashing over language and terminology associated with supplementary materials and our eventual creation of the extension. The extension is not part of the official JATS specification; it is a local extension that will be made publicly available for community use and discussion.

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