Plenary sessions | Main meeting room
The Future of Reference Processing
Lateiner, Ulysses S. (ELS-CMA): Lake Tahoe went from being on fire the last four months to having 2 feet of snow. Whee!
Sylvia Hunter (Inera): Yikes!
Debbie Lapeyre: LOVE SNOW! WE got inches of rain last night. Nice now in Washington, DC
Lateiner, Ulysses S. (ELS-CMA): will the 1100 JATS/PMC session cover eXtyles deposition to PMC?
Lateiner, Ulysses S. (ELS-CMA): or is that part of the immediately upcoming session?
LittlePN: Good morning all!
Joni Dames (Inera): Whose Content at 11 is about wrangling XML for PMC (and elsewhere), and will briefly mention the eXtyles XML deposits to PubMed and Crossref
Jennifer Seifert (Inera): @Ulysses we will discuss PMC deposits somewhat at the 11:00 session but I do not think it will be part of the 10:00 session
Jennifer Seifert (Inera): Joni beat me to it!
Lateiner, Ulysses S. (ELS-CMA): ????
Ken Rawson: For Gary, will a report go back to the author about the quality of their article, as well as to an editor?
Luciano Panepucci: I have a magic spreadsheet that does this references breakdown semi automatically! 🙂
Jo Ripoll (Inera): Ken, we’ve noted your question for the Q&A at the end
Gary Spencer: @Ken—ReX doesn’t currently generate a report for the author, but this is on our roadmap!
Ken Rawson: For Simon, have journals that appeared on your predatory list challenged their listing?
Peter Olson: For Simon: How does a potentially predatory journal come to Cabells’ attention, and/or how do you go about selecting journals to assess as being potentially predatory?
Luciano Panepucci: Gary: I feel that most authors do bad practices due to a lack of information and time for proper due diligence during writing. Exposing ReX while the author is actually WRITING their manuscript could potentially educate them and make it easier for journals staff down the stream. ReX could return information pertaining to the current manuscript section being edited (titles, keywords, COI statements, references etc.). Have you considered enabling the ReX API in manuscript authoring platforms?
Luciano Panepucci: Simon: I’m seeing predatory PUBLISHERS trying to acquire legitimate journals. I see two scenarios: 1) predatory publishers actually trying to become legit—less likely I fell, or 2) trying to look legit while turning legit journals into predatory. How does that affect the Cabells alerts? Does Cabells reevaluate journals after adding flagging them as good/bad?
Lee Calibeo: When a predatory journal is removed (after new ownership), is the removal date-based . . . articles published under the previous owner are still flagged?
Luciano Panepucci: Gary: You add 50 new journals per month?!?!
Ken Rawson: With all of the additional ethical information becoming more available to editors, will their workloads increase with having to sort through more information about each article? I know this may be controversial, but I think it’s worthy of discussion.
Luciano Panepucci: we’ve received many Acquisition Proposals from pulsus.com
Luciano Panepucci: none accepted for our journals
Luciano Panepucci: Good question!!!
Sylvia Hunter (Inera): I believe flagging is on the journal level not the article level
Sylvia Hunter (Inera): Would be interesting to add some kind of date filter…
Liz Blake (Inera): I think that may be a question for Inera to address (Lee’s question about date-based alerts)
Robin Dunford (Inera): Yes, I can already hear Igor’s brain whirring
Simon Linacre: To Luciano—it’s not 50, it’s 150 new journals added a month!
Luciano Panepucci: ????????????????????
Gary Spencer: @Luciano—we aren’t adding 50 journals per month to ReX yet. Our current peak is about 20-25 journals per month, but our goal is closer to 80 journals per month. We expect to hit that goal in the next 2-3 months.
The JATS Family Grows: The Latest on JATS, BITS, and STS
Sylvia Hunter (Inera): This is definitely the right audience for standards weenies ????
Gary Spencer: (I may have misinterpreted the question. 🙂
Igor Kleshchevich (Inera): Yeah, the essential question is whether an article has been through peer review. Would be great if we had the information on status change for a journal…
Sylvia Hunter (Inera): Would I be correct in supposing that journals sliding from legit to predatory is much more common than the reverse?
Ron Keller: Verifying a start date for predatory behavior sounds like it would be labor intensive.
Ron Keller: (But yes, article-level identification would be valuable information if a journal changes status.)
Robin Dunford (Inera): @Luciano—by contrast, MEDLINE appears to have added 22 journals this YEAR
Robin Dunford (Inera): (from https://www.nlm.nih.gov/medline/medline_new_titles.html)
Robin Dunford (Inera): @Ron—I think (if it happened on the Inera side) we could only base the cut-off on when the journal was added/removed from Cabells
Ron Keller: That’s a reasonable choice.
Luciano Panepucci: @Robin—yes. But that is expected. MEDLINE does a full in-depth peer-review of a journal’s institutional information (policies and guidelines) and confront it with actual published content to see if the journal adheres to it ‘s stated policies and with good practices.
Igor Kleshchevich (Inera): E = mc² can be done without any markup at all, since “superscripted 2” is a character 🙂
Robin Dunford (Inera): Of course—but the difference in scale is quite dramatic
Luciano Panepucci: @Robin—oh yes. VERY!!! TERRIFYING actually.
Luciano Panepucci: @Robin—It would be interesting to know the DOAJ new journals growth since they claim to index open access non predatory.
Ron Keller: I like that documentation structure. Thank you!
Susie: Will <inline-media> be available in BITS
Robin Dunford (Inera): DOAJ just went through 17,000 titles, but I don’t see historic data from a quick search
Jo Ripoll (Inera): Question noted for the Q&A, Susie!
Sylvia Hunter (Inera): I have never heard the term “smershy” but will be adopting it immediately
Igor Kleshchevich (Inera): Yeah, love “smershy”!
Robin Dunford (Inera): Sounds ominous in Russian though
Ron Keller: @Robin 🙂
Igor Kleshchevich (Inera): @Robin: very true :-):-):-)
Robin Dunford (Inera): @Debbie—No tagset-family for NLM Book?
Robin Dunford (Inera): Now we need them in BITS…
Robin Dunford (Inera): The new documentation looks great, btw
Sylvia Hunter (Inera): We wrote about the new tag libraries in the Inera newsletter a while back: https://www.inera.com/newsletter/march-2021-newsletter/#sec2
Sylvia Hunter (Inera): You’ll find links in there to go check it out
Igor Kleshchevich (Inera): The documentation looks great
Ron Keller: We are changing JATS standards and adding new features in the very near future, and I am excited to take advantage of that new documentation.
Sylvia Hunter (Inera): It’s so cool!
Igor Kleshchevich (Inera): ????????????
Luciano Panepucci: @Sylvia—I honestly don’t know how to weight that for individual journals. My main concern is with publishers acquiring legit journals.
Concurrent 1A: What’s New at NISO?
Sylvia Hunter (Inera): https://www.niso.org/events
Sylvia Hunter (Inera): https://niso.plus/
Sylvia Hunter (Inera): The acronym is CORREC 🙂
Sylvia Hunter (Inera): Yes we will!
Sylvia Hunter (Inera): The slides will be linked from https://www.inera.com/user-group-meeting/ in about 5 minutes
Sylvia Hunter (Inera): email@example.com
Sylvia Hunter (Inera): firstname.lastname@example.org
Robin Dunford (Inera): Did we get the definition of CORREC?
Sylvia Hunter (Inera): Thank you Robin! I was looking for that link
Concurrent 1B: Whose Content Is It Anyway? JATS Markup for PubMed Central and You
Debbie Lapeyre: Comment not question: Valid does not mean correct, but it sure is a good first step!
Luciano Panepucci: We use style checker all the time
Luciano Panepucci: both PMC and Scielo
Kathryn Miller (she/her): yes!
Debbie Lapeyre: Schematron are us
Ron Keller: We don’t use style checker, but it sounds like something we should be doing.
Luciano Panepucci: I read the mailing
Susie: as well as online there is a downloadable version as well
Luciano Panepucci: yes
Jennifer Seifert (Inera): https://www.ncbi.nlm.nih.gov/pmc/tools/stylechecker/
Debbie Lapeyre: There is a PMC style checker mailing list. Really? Thank you, I did not know.
Susie: Tagging Guidelines Email List. Both the Tagging Guidelines and Style Checker are updated periodically, in an effort to make the PMC archive more robust, improve the quality of the XML submitted, and ensure stability for future retrieval. PMC announces these changes through our pmc-tagging-guidelines email list. Go to the list information page to subscribe.
E. Andrew Jessup: Stylechecker: yes! Mailing list: yes!
Susie: You can subscribe on the PMC style checker page
Stacy Lathrop: Is there an Off-the-Shelf BITS product that meets all PMC style checks—the has been an issue for Bookshelf submitters
Stacy Lathrop: Bookshelf also has Schematron checks for BITS submitters to Bookshelf based on discussions with those content providers
Luciano Panepucci: single XML: dream on
Jennifer Seifert (Inera): Hi Stacy! We don’t have an off the shelf BITS product, primarily because the content elements for books and reports can vary so dramatically
Lateiner, Ulysses S. (ELS-CMA): does eXtyles itself contain a mechanism that deposits to PMC? or is eXtyles merely capable of exporting PMC-compatible XML?
Stacy Lathrop: Is there confusion between PMC (JATS) / Bookshelf (BITS) style checks—do we need to make this clearer?
Jennifer Seifert (Inera): @Ulysses, stay tuned… 😉
Jennifer Seifert (Inera): Stacy, I’ll add that question to the Q&A at the end
Luciano Panepucci: We have two export filters in use: JATS PMC and Scielo.
Stacy Lathrop: How can NLM/NCBI make metadata easier for downstream indexing in PubMed?
Debbie Lapeyre: JATS checking can be moderately strict. Books vary too much for that kind of strictness.
Stacy Lathrop: Bookshelf does got through PMC style checks though, fyi. We ask submitters to do those checks. On top of that Bookshelf add custom submitter schematron checks for our conversions.
Luciano Panepucci: We have to add the collection thing
Luciano Panepucci: We have to add the collection thing do pub-date.
Jennifer Seifert (Inera): Hi Luciano! I’ve noted that ????
Luciano Panepucci: We’ve resolved by adding de collection thing to the Update Document dialog.
Monica Mungle: At the JAMA Network, we use “for the” group and “and the” group to differentiate group members who are not authors and those who are authors.
Luciano Panepucci: yes
Debbie Lapeyre: WE know JATS4R
Stacy Lathrop: For PMC/NCBI/NLM we need for citations to distinguish between—on behalf of, a collab to be listed in the main citation AND / OR a collab that has collaborative authors—just noting this as it has been unclear at least for books / reports submitted to Bookshelf
Luciano Panepucci: We’re not using them YET for they are not enforced by our target databases.
Luciano Panepucci: (the jats4r I mean)
Debbie Lapeyre: yes yes yes Schematron, we have written many for clients. They do want amazingly detailed checks, for different lifecycle stages
Luciano Panepucci: One annoyance is that for PMC, we need to update pub-date to make sure it is equal to the publisher stated pub date in their website.
Debbie Lapeyre: How do you tag the “author pronouns” in JATS? There is no specific element or attribute for that.
Liz Blake (Inera): You two can lobby me!
Joni Dames (Inera):
Stacy Lathrop: Just note, Bookshelf citations to PubMed are based on the metadata from the full text BITS, and in some case for JATS too …
Debbie Lapeyre: OOOOh the modules do the deposit as well!
Plenary sessions | Main meeting room
Debbie Lapeyre: Always look forward to these!
Sylvia Hunter (Inera): So do we 😀
Sylvia Hunter (Inera): Still no Canada goose emoji 🙁
Nettie Lagace: 😀
Robin Dunford (Inera): (deer in a hole). hmm…, hasn’t made it into Zoom yet
Debbie Lapeyre: Deer should be careful, those gophers are fierce!
Robin Dunford (Inera): ????
Debbie Lapeyre: Why do authors not use @ref-types? SAY you are software.
Robin Dunford (Inera): My suspicion would be that, even if a journal asked authors to do that in their I for A, many/most authors would not
Robin Dunford (Inera): If the reference points to a URL, they may regard that as sufficient
Ron Keller: Agreed. You can provide information for authors, but you’re still just herding cats.
Luciano Panepucci: Vendors checking and researching all erefs is expensive.
Robin Dunford (Inera): Agreed. Even our URL Validation function only tells you that the URL is live
Nettie Lagace: will look into that, Bruce! 🙂
Luciano Panepucci: I did not know of that recommendation. It’s great and should be spread and used.
Jennifer Kemp: We at Crossref do get a lot of questions about data citation—many publishers are still working that out. Some information for those interested https://www.crossref.org/documentation/reference-linking/data-and-software-citation-deposit-guide/
Sylvia Hunter (Inera): Once upon a time, I asked a composition vendor to typeset an ENTIRE JOURNAL ISSUE both with and without DOIs in the reference lists, because that was the only way to convince the journal editors that including DOIs would not increase costs by increasing page count
Sylvia Hunter (Inera): I will not name the journal or the editors but like
Robin Dunford (Inera): ????
Sylvia Hunter (Inera): Me, I know!!
Debbie Lapeyre: WOW Sylvia, just WOW!
Sylvia Hunter (Inera): … but Bruce may have been the one who explained it to me ????
Luciano Panepucci: it’s sad. Publishers maybe want to save page charges from their vendors?
Sylvia Hunter (Inera): @Debbie RIGHT?! In their defence, it was 2008
Sylvia Hunter (Inera): BUT STILL
Sylvia Hunter (Inera): Oh I have an even better story!!
Joel T. Luber (he/him, Duke Univ. Press): Love the MS DOS mention just below. lol
Robin Dunford (Inera): Some editors in chief and boards are obsessed with page counts, in my experience—always good to point out the full economic cost of providing a less useful reading experience
Sylvia Hunter (Inera): My stepdad (a retired electrical engineering professor) recently published a book with a publisher I will not name, and my mum (an editor) helped him with the publishing process, and they received two separate sets of author instructions WHICH DISAGREED WITH EACH OTHER ON MULTIPLE AXES
Luciano Panepucci: As for instructions being out dated I STILL see Word version 6 or worse … Publishers seem to not care for the journal specific instructions.
Sylvia Hunter (Inera): One set of author instructions also said “use Chicago style” and then gave multiple reference examples that were … not in Chicago style
Jennifer Kemp: Can’t say I am surprised really!
Robin Dunford (Inera): Journals insisting on a reference style is so 20th century!
Stacy Lathrop: How can you make a platform-agnostic system to avoid this blockers—I agree they should not exist at this point in time. But also, if people are trying to get scientific findings out via pre-print earlier, how does that fit in an agnostic infrastructure?
Jo Ripoll (Inera): That’s a great question, Stacy. I’ll make sure we get to it in the Q&A
Joel T. Luber (he/him, Duke Univ. Press): These instructions are also an equity issue because of what sorts of people can (or try) to get away with not following the instructions and those who don’t feel they’re able to do that.
Liz Blake (Inera): Agreed, Joel
Luciano Panepucci: Bruce is 1000% right.
Robin Dunford (Inera): Do publishers/societies still employ the people who wrote their instructions, or the people who know what they were trying to achieve? I know my former employer does not, as a sample size of 1
Jennifer Kemp: Thank you, stay well all!
Sylvia Hunter (Inera): @Robin my guess is nope.
Lateiner, Ulysses S. (ELS-CMA): Thanks Inera for an informative + entertaining event as always. Everyone please stay healthy!
Luciano Panepucci: I help lots of journals to update their policies and preparation guidelines. I already focus on making sure they enforce the editorial policies instead of format. But I’ll get more radical and start advocating for that.
Joel T. Luber (he/him, Duke Univ. Press): When I worked at a publishing services provider, our customer societies owned their own websites, and we didn’t have any control over the author instructions they put up. ????♂️
Luciano Panepucci: Maybe not all reference managers support those kind of references.
Sylvia Hunter (Inera): I had to share that story because I have heard kvetching about this book every Sunday evening on the phone for AN ENTIRE YEAR
Robin Dunford (Inera): There is also a danger of asking for information for the sake of it—do we need to know a reference is a blog vs some other sort of webpage? Authors are overloaded already
Ron Keller: As someone who does production, I would rather have your source files than a PDF.
Robin Dunford (Inera): @Ron amen to that!
Debbie Lapeyre: True, authors are overly burdened, but DATA and SW citations are different
Robin Dunford (Inera): Because of the machine-readability implications?
Debbie Lapeyre: Data as being foundational. Yes, I guess SW is not as special, but the processing requirements are very different
Robin Dunford (Inera): right
Sylvia Hunter (Inera): @Ron hard agree!
Kevin O’Donovan: At some point in the future, will we do away with volume, issue, and page numbers (and just stick with a single electronic ID for each article)?
Debbie Lapeyre: Some publishers already have. They do not publish in issues at all.
Monica Mungle: Thanks Inera! Great to see everyone.
Kevin O’Donovan: Thanks for a great meeting!
Robin Dunford (Inera): But please follow the NFAIS guidelines for your article IDs!
Liz Blake (Inera): Thanks everyone for coming and engaging with us! 🙂
Annie Gering (she/her): Thank you! Great XUG, as ever.
Ron Keller: Thanks, everyone!
Robin Dunford (Inera): Thanks everyone—hope to see many of you in person in 2022…
Luciano Panepucci: THANK YOU!!!!
Louise Adam: Thanks, everyone. Always great to be at XUG!
Lauren Kmec: Thank you! I really enjoyed the meeting.