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JATS and the Standards Ecosystem


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you very much for your good afternoon everyone on made a lot of time on the internet there's this year we've had in the
past but I wanna talk just for about 15 minutes about Jackson the standards ecosystem all when a few of us sat down at this point a dozen years ago to
start developing Jackson was released its own little island we had basically 2 missions that we had so 1st with creating a better DTD for public central and the 2nd was creating a DTD that will work for work on an archive that ended up being located with cortical all over time however even though those objects is built on standards like XML and unit code in math em out hot gas itself has so wasn't completely in Ireland it's become much less of
an island because it works within on an ecosystem particularly for the metadata so we're just started out as a markup solution would it's morphed into is what I call now the workflow solutions that by integrating not just the full text content of rich metadata which at facilitates is 1st of all all of the metadata our transmittal of a submission so I think most of the major online submission peer review systems at this point can transmit the metadata to you in the exact suggests like form it facilitates and and production activities are think about the presentation from my this morning where they said we do everything in between pure view and online hosting and so Jackson facilitating that all intermediate workflow and finally it facilitates distribution of metadata customers so what's happened is Jack and that's
also have become central to the entire workflow so so what I wanna to is briefly touched on a number of standards and projects some of which they directly interact art with chapter and others on this list of things that if you're involved with
chatter involved journal publishing you should know about even there's not necessarily direct connection
and I'm just gonna go through these off very quickly our my slides which will be posted you have your else for part the 1st is the supplemental journal article materials project this is a joint on my so and face project the publisher recommended practice last year could children and family published a supplemental material OK I'm seeing at least a 3rd of and maybe half
hands of the room go up if you publish supplemental materials you need to read this there's a lot of really valuable information on in
terms of how it integrates with objects I recommend you be here tomorrow morning properly I think it's 9 o'clock at the 1st presentation tomorrow all wrapped carrying Kimberly talking about on integrating this recommended practice into jets on the 2nd 1 is
working on work it has really taken off in the last year this is to create a persistent and unique identifier for every author so you know on Johnson number 1 suggests that members to from John Smith number about 10 thousand and 20 degrees are this is becoming increasingly important in the research world were particularly funders 1 of track of the officer involved in grants from the point of submission to the grant to all the publications that are published under that grant and by being able to track the authors with work and that's 1 of the things they can do that for those of you who haven't upgraded the Jets 1 . 0 working on finding with the people that I work with on a regular basis is 1 of the biggest reasons for upgrading ought to 1 . 0 all because they contribute ID element is in there are it's not just for work and there's a type attrib uted can say all which kind of an author ideas whether it's working or anything else that might be an easy for example aren't you can specify that are in fact just was in last power I saw an informal request to the working group that . 80 are verified activate the added intravital because working there is an important concept of verification all this is a picture from
often work at presentation last fall workshop that was in our Washington on know this work ideas popping up all over the place and 1 that I regret not showing up here there is the laser pointer here on the on the XML to cross the art there's no work at ID but 1 that and that's a critical part of this all because crossref really wants to have been working these in deposits there and so the ID the idea sorry not the idea behind the ID is the it would be added in at the submission stage it carries through into your jets XML on in production and then is available for any of the metadata transmissions you do project this is
probably 1 of the lesser-known our standards of my talk about a project i this is about presentation and identification of e-journals online this is an ISO project on the 2 recommended practice detection and publishing this basically says if you're putting up a website with journal there's some critical information you wanna make sure you put on that website on this is
just 1 picture off from the pi j recommended practice on this particular publisher as are being written very careful about putting up there I have to send the full title the abbreviated title the codon and so on on what they don't have the title history but there are other pictures I could have put in where you can click a link and get the entire title history you can very quickly get to the editorial board I don't know how many of you ever gone to the website of the journal and just tried to find the highest ascent of that show because you might wanna know it it's shocking how many journals don't in fact have that information easily accessible so what is you putting your content online I do recommend you take a look at pi j the interaction with cats here is most to this is metadata that you may well want in your jets files not all that you wouldn't necessarily what the title history orbit is something to think about in terms of your overall metadata workflow
all this is an older project the journal article version project again tonight so project this was to develop a set of recommended terms that could be applied to iterations of an article's cycle but the reason I put this in his because that's undergoing some addendum work now to set up on a set of better terms for our articles in proof category crossref injects on there's
a lot going on in terms of interaction between Russia from Jack to process started the basic idea was that for any given article you want to provide cross-traffic he metadata authors tidal volume issue page on ends the deal why neural and that was pretty much words stop the process has grown tremendously it's become this incredible central hub for publishers for all kinds of cross publisher initiatives
onto the first one I wanna mention is cross mark again this is when it doesn't have to do as much with Jax all but I wanna highlighted
because 1 of the areas where on unfortunately we're seeing a lot growing in sort of push to publish rapidly we're seeing more and more corrections and retraction anyone's ever looked at . 5 arrestees these retraction watch on that is by a publication is growing not shrinking on if you're content is indexed in PubMed med it's great that they do a phenomenal job of keeping track of corrections and retraction but if you're not in life Sciences you're not in public there is no central clearinghouse for a being able to electronically keep track keep track of retractions were for example you could query reference and say is is referenced in this is something that's been retracted while cross mark we now have the the ability to do that 1 of the key things however with cross mark is you've got the metadata into cross and a lot of people have the impression that OK I'm just do this going forward Molina put the cross mark information my PDF going forward but guess what you can put your metadata into cross-traffic even if you don't update the old pdfs and this is important because what I personally love to see what people do is go
back and put the critical correction information going back as far as you can in the class have even if you don't update your PDF because then people can very quickly find out information about published content what 1 quick piece of breaking news on cross mark up till now there has not been a standard vocabulary for correction types that is something the cross-reference now working on to keep your eyes open for them cross-track metadata services in this a suite of tools they
allow metadata mining through crossref on there are a couple of jets implications for this in terms of what you can now deposit crossed to remember our moment I like this to just a few key elements the crossref was originally set up to handle in deposit now there's a whole suite of visual elements including 1st of all the cross check deposit schema now supports math amount to particularly if you're in engineering or physics and you have our equations as part of article titles you can deposit those with the math amount the 2nd thing is the cross F. deposits schema now supports the entire Jats abstract not so what that means is you can actually deposit the abstracts of the articles you published in the cross which means that people can then text and data mining through cross-track metadata services part that's 1 more way you can expose your content to our people throughout the world
fun draft is initially the taking off very quickly with crossref are I talked before with orchid how a lot of funders are more interested than ever in tracking the life cycle of the grant to the publication and so 1 of the things funders would like to see is the metadata for all the funding information particularly the funding agency in the contract number tied together now the NLM DTD years ago we did have support for this 1 of the changes in going from 2 . 3 to 3 . 0 0 and then into Jack's was a rework of that funding models so it's actually much richer and more robust and that complain really well with cross-reference terms of depositing information across the if you are looking at just 1 . 1 the 1 on 1 of the newest elements of institution around and as part of that funding information you can now have institution ideas along with an institution name inside of our institution wrapped element and that can be used both within the affiliation if you just want to mark the institutions within a variational or more important in this context it can be used within funding sources so that you can uniquely identify the institutions and does have a our list of recognized funding agencies this is a list they got from Elsevier it's got about 4 thousand initial information about 4 thousand agency all skip ahead for a
moment that this is not complete as you can imagine there are more than 4 thousand funding agencies in the world the official have of some extremely acknowledgements that I pulled from articles on public central last on December anything in green here was an agency that is actually recognized within the crossref set orange means it's close but not exact matching red means it wasn't actually in the cross traffic data so if there is an agency that
part is not annotated it's listed within your article content you can reported in at the photograph registry . html it is quickly to show you an idea here this is the fun draft workflow and the key thing if you look down between the 3 and 6 on the bottom of publisher production systems the idea of integrating this metadata which means getting this metadata oftentimes from a submission system into your jets XML and then being able to push it out on the back the license metadata is another
area that's a hot topic these days if I wanna make sure I finish sometimes you get your full Blake because the next paper after the break is 1 that I heard at the Jets usually being that held last October and jets can't it's a great paper it really makes incredibly important points about inconsistent XML and 1 of the areas it really honed in on inconsistencies license metadata on this is critically important to make the content machine readable it's no longer as was pointed out a couple of other presentations today it's no longer about having human readable XML that's about having XML that machines can act on so I recommend you
come back promptly after the break for Daniels that right yes thank you for Daniels paper he's waving his hand up there on crossref has added are an element against their deposits schema for license traffic information where you can essentially put Creative Commons license information into your cross-traffic positive just as you can put that Creative Commons license information into your gas XML files so again you can go from a concept amount to be crossed deposit very simply and easily with a than Excel's XSLT transform and so this is something you should be aware of and what this means is if you put that correct information in there and combine that with the
crossing of metadata services you can then start to an automatic mining of what's freely available under what kinds of this all plays into another active project that's going on with nice
so called the open access metadata and indicators project because if you think about it and have creative commons which states in a very clear fashion what the licensing terms on but what it does instead is what the open access availability it would be and so the goal of this project is to harmonize all of this and the implications for Jackson's this is 1 of the sort of stay tuned to this space Our speech into this channel messages is there will probably be some best practices coming out about how to use the licensed and open access elements that are injected so stay tuned to this I I'm not sure exactly where this is gonna land but the people who were working on this project are actively talking to the Jets Working Group and so we are trying to make sure that we all stay on the same page but I mean you know all
courses OK about a 3rd of the hands and for those of you don't know chorus is a response to the broader US government mandate that not just life sciences content that and this NIH-funded but all government-funded research be freely accessible to the public however unlike government central where the government built infrastructure for this and and I just had the resources to do it a lot of agencies to the government don't come to me don't have the resources to be able to build this kind of infrastructure and of course is an arrangement are organized by publishers to be able to expose the open access information much more easily and make it discoverable on the publisher's website which we
really need is this works based on existing infrastructure so what we've got in the upper left-hand corner is the publisher manuscript workflow this is your production workflow and then the last circle that filled in on just below that is the metadata deposits and what is what is relying on metadata posits fun direct cross-power work is licensed graphs and ultimately haven't DOI links for all of this down at the bottom if all of these pieces of infrastructure put together courses can work so the critical part of pulling together course for any other major initiatives were at an end and workflow these days
comes down to 1 of the next steps you're going to do is published to my takeaway recommendations her 1st of all review some of the standards so far that I've talked about if you want familiar with them already and think about what those metadata requirements are then what you wanna do is figure out the workflow for the best medical data integration path that in of itself is a totally separate talking to nontrivial set of issues but you wanna think carefully about how you want to that and consider as part of this the upgraded jets 1 . 1 1 unless you're to Enel and 2 points here earlier the upgrade should be be fairly painless because everything is pretty much backwards compatible in implementing revised metadata workflows think really carefully about what you're QA steps metadata to is probably the single most important but in some cases most overlooked part of quality assurance of x amount you wanna think carefully about how you integrate that ultimately what you want do His provide rich metadata to cross the graph to problematic government central to any of the Ole funders works goes with they 1 exposed or any other organizations downstream the consume your content some of which we may not have even thought of it again you may hear about 1 of those after the break so so thank you very much and
I'm happy to take any questions I have to which and that this
is not a question of heavy audience today
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Formal Metadata

Title JATS and the Standards Ecosystem
Title of Series JATS-Con 2013
Part Number 8
Number of Parts 16
Author Rosenblum, Bruce
License CC Attribution 3.0 Unported:
You are free to use, adapt and copy, distribute and transmit the work or content in adapted or unchanged form for any legal purpose as long as the work is attributed to the author in the manner specified by the author or licensor.
DOI 10.5446/21799
Publisher River Valley TV
Release Date 2016
Language English
Production Place Washington, D.C.

Content Metadata

Subject Area Information technology
Abstract JATS, BITS, and publishing live in an ecosystem of interrelated standards and initiatives. If you don't know what the acronyms ORCID, PIE-J and JAV stand for, this talk will describe what they are and why JATS implementers should be familiar with them and many standards, recommended practices, and other initiatives in the JATS neighborhood.

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