Getting From Word to JATS XML

In this blog Bill Kasdorf, Principal, Kasdorf & Associates, LLC talks us through a perennial problem and the different approaches to addressing this:

It is a truth universally acknowledged that journal articles need to be in JATS XML but they’re almost always authored in Microsoft Word.

This is not news to anybody reading this. This has been an issue since before JATS existed. Good workflows want XML. So for decades (yes, plural) publishers have been trying to get well structured XML from authors’ manuscripts without having to strip them down to plain text and tag them by hand. (This still happens. I’m not going to include that in my list of strategies because nobody thinks that’s a good idea anymore.)

There are four basic strategies for accomplishing this:
• Dedicated, validating XML editors.
• Editors that emulate or alter MS Word.
• Use Word as-is, converting styles to XML.
• Editors that use Word as-is, with plug-ins.
Here are the pros and cons of these four approaches.

Dedicated, Validating XML Editors

This is the “make the authors do it your way” method. The authors are authoring XML from the get-go. And not just any XML. Not even just any JATS (or whatever XML model). Exactly the specification of JATS that the publisher needs, conforming in every way to the publisher’s or journal’s style guide and technical requirements. This strategy works in controlled authoring situations like the people developing technical documentation. (They’re probably authoring DITA, not JATS.) They’re typically employees of the publisher, and the document structures are exactly the same every day those employees show up to work.

I have never seen this strategy successfully employed in a traditional publishing context, although I have seen it attempted many times. (If anybody knows of a journal publisher doing this successfully, please comment. I’d like to know about it.) This doesn’t work for journals for two main reasons:
1. Authors hate it. They want Word.
2. They have already written the paper before submitting it to the journal. The horse is out of the barn!

Editors that Emulate or Alter MS Word

This always seems like a promising strategy, and it can work when it’s executed well in the right context. The idea is to either let authors use Word, but make it impossible for them to do things you don’t want them to do (like making a line of body text bold when it should be styled as a heading), either by disabling features in Word like local formatting or by creating a separate application that looks and acts a lot like Word.

I have seen this work in some contexts, but for authoring, I’ve seen it fail more often. The reason is No. 1 above. Despite being a lot like Word, it’s not Word, and authors balk at that. These are often Web-based programs, and authors want to write on a plane or the subway. And there’s always No. 2: most journal articles are written before it’s known which journal is going to publish it.

This strategy can work well, though, after authoring. Copyeditors and production staff can use a structured tool like this more successfully than authors can. We’re seeing these kinds of things proliferate in integrated editorial and production systems like Editoria, developed by the Coko Foundation for the University of California Press, and XEditPro, developed by a vendor, diacriTech.

Use Word As-Is, Converting Styles to XML

This is by far the most common way that Word manuscripts get turned into XML today. A well designed set of paragraph and character styles can be created to express virtually all of the structural components that need to be marked up in JATS for a journal article. This is done with a template, a .dotx file in Word, which, when opened, creates a .docx document with all of the required styles built in. And since modern Word files are XML under the hood, you can work with those files to get the JATS XML you need.

The question is who does the styling, and how well it gets done.

Publishers are sometimes eager to give these templates to their authors so they can either write or, post-authoring, style their manuscripts according to the publisher’s requirements. Good luck with that. The problem is that it’s too easy to do it wrong. Use the wrong style. Use local formatting (see above). Put in other things that need to be cleaned up, like extra spaces and carriage returns. Somebody downstream has to fix these things.

Those people downstream tend to be trained professionals, and it’s usually best just to let them do the styling in the first place. This is how most JATS XML starts out these days: as professionally styled Word files. Many prepress vendors have trained staff take raw Word manuscripts and style them, often augmented by programmatic processing to reduce the manual work. These systems, which the vendors have usually developed in-house, also typically do a “pre-edit,” cleaning up the manuscript of many of those nasty inconsistencies programmatically to save the copyeditor work.

This is also at the heart of what I would consider the best in class of such programs, Inera’s eXtyles. Typically, a person or people on the publisher’s staff are trained to properly style accepted manuscripts; eXtyles provides features that makes this easier to do than just using Word’s Styles menu. Then it goes to town, doing lots of processing of the resulting file based on under-the-hood XML. It’s primarily an editorial tool, not just a convert-to-XML tool.

Use Word As-Is, With Plug-Ins

This is not necessarily the same as the previous category, but there’s an overlap: eXtyles is a plug-in for Word, and the resulting styled Word files can just be opened up in Word without the plug-in by a copyeditor or author. But that approach still depends on somebody having styled the manuscript, and subsequent folks not having messed up the styling. It also presents the copyeditor (and then usually the author, who reviews the copyedits) with a manuscript that doesn’t look like the one the author submitted in the first place.

This tends to make authors suspicious—what else might have been changed?—and suspicious authors are more likely to futz. That’s why in those workflows it’s important to use Tracked Changes, though some authors realize that that can be turned on and off by the copyeditor so as not to track every little punctuation correction that’s non-negotiable anyway.

An approach that I have just recently come to appreciate is what Ictect uses. This approach is not dependent on styles. As much as I’ve been an advocate of styles for years, this is actually a good thing. Styles are the result of human judgment and attention. When done by trained professionals, that’s pretty much okay. But on raw author manuscripts—not.

Ictect uses Artificial Intelligence to derive the XML not from the appearance of the article, which is unreliable, but on the content. Stop and think about that a minute. Whereas authors are sloppy or incompetent in getting the formatting right, they are pretty darn obsessive about getting the content right. That’s their paper.

Speaking of which, in addition to not changing the formatting the author submitted, Ictect doesn’t change the content either. The JATS XML is now embedded in that Word file, but you only see that if you’re using the Ictect software. After processing by Ictect, the document is always a Word document and it is always a JATS document. To an author or a copyeditor it just looks like the original Word file. This inspires trust.

I was initially skeptical about this. But it actually works. Given a publisher’s style requirements and a sufficiently representative set of raw author manuscripts, Ictect can be set up to do a shockingly accurate job of generating JATS from raw author manuscripts. In seconds. Nobody plowing through the manuscripts to style them.

There have been tests done by large STM publishers that have demonstrated that Ictect typically produces fully correct, richly tagged JATS for over half of the raw Word manuscript files submitted by authors, and over 90% of manuscripts can be perfected in less than ten minutes by non-technical staff like production editors. The Ictect software highlights the issues and makes it easy for publishing staff to see what the problem is in the Word file and fix it. That’s because the errors aren’t styling errors, they’re content errors. They have to be fixed no matter what.

In case you think this is simplistic or dumbed-down JATS XML, nope. I’m talking about fully expressed, granular JATS, with its metadata header and all the body markup and even granularly tagged references that enable Crossref and PubMed processing. Not just good-enough JATS. Microsoft Office 365 is not exactly a new kid on the block now, but journal publishers have not made much use of it. As things evolve naturally, more and more authors are going to use Office 365 for peer review, quick editing, corrections and even for full article writing. Since Ictect software creates a richly tagged Word document that can be edited using Office 365, it opens up some interesting workflow automation and collaboration possibilities, especially for large scale publishing.

And if you need consistently styled Word files, no problem. Because you’ve got that rich JATS markup, a styled file can be generated automatically in seconds. For example, in a consistent format for copyediting (I would strongly recommend that), or a format that’s modeled after the final published article format. Authors also really like to see that at an early stage. It’s an unavoidable psychological truism that when an author sees an article in published form she notices things she hadn’t noticed in her manuscript. So you can do both: return the manuscript in its original form, and provide a PDF from the styled Word file to emulate the final layout.

All of the methods I’ve discussed in this blog have a place in the ecosystem, in the right context. I haven’t mentioned a product that I wouldn’t recommend in the right situation. For example, you might initially view Ictect as a competitor of eXtyles and those home-grown programs the prepress vendors use. It’s not. It belongs upstream of them. It’s a way to get really well tagged JATS from raw author manuscripts to facilitate the use of editorial tools, without requiring manual styling. It’s the beginning of an Intelligent Content Workflow. It’s a very interesting development.

Bill Kasdorf is Principal of Kasdorf & Associates, LLC, a consultancy specializing in accessibility, XML/HTML/EPUB modeling, editorial and production workflows, and standards alignment. He is a founding partner of Publishing Technology Partners 

Website: https://pubtechpartners.com/

Twitter: @BillKasdorf

To find out further information on Ictect visit: http://www.ictect.com/ 

or register for one of their free monthly webinars at: http://www.ictect.com/journal-webinars

Navigating the safe passage through the minefield of predatory publishing

Philip J Purnell and Mohamad Mostafa, Knowledge E

Like many of the world’s scholars, young researchers at Al-Nahrain University in Iraq have been told they need to publish research articles in academic journals in order to progress in their careers. Aware of the low acceptance rates and lengthy publication delays in traditional journals, many turn to relatively recently launched open access journals that market their quick turn-around and low publishing charges. Dr. Haider Sabah Kadhim, head of Microbiology at the university says these young researchers are being duped into paying 100 – 200 USD on the promise of fast-track publication within one week. He has seen countless academics proudly show their published papers only to be told they won’t count because the journal isn’t on an approved list. Dr. Haider expressed his worry about the long term harm this publishing practice could cause to their careers.

The same pressure is felt by the research community across the region, Egyptian Assistant Prof. Hossam El Sayed Donya teaches medical physics at faculty of science King Abdulaziz University in Saudi Arabia. He sees similar challenges and says that some publishers boast of being indexed the top databases like Web of Science, Scopus, and MEDLINE, having Journal Impact Factors and that they assign digital object identifiers (DOIs) to all published articles. Often these promises turn into disappointment when the researcher realises their article cannot be found in the databases, the journal doesn’t really have an impact factor or that the DOI is not deposited in the Crossref database. Prof. Hossam said there is a need for information and guidance in both English and Arabic for early career researchers that teach them the signs to look for in a good journal/publisher and those to avoid.

The dilemma

Modern scholars are coming under increasing pressure to demonstrate their academic productivity, by which their output is determined by the number of research papers they have published and their impact is determined by counting the citations to each researcher’s articles. Indeed, universities and promotion committees often set targets and thresholds for academic progression based on publications and citations. Universities do this because they also operate in an increasingly competitive space and are themselves responding to pressure for a good performance in the international university rankings such as Shanghai, Times Higher Education, QS and others that count publications and citations to the articles published by the entire university faculty.

One enviable mark of a high-quality journal is being indexed in a renowned database such as the Web of Science, Scopus or MEDLINE. An even more elite group of around 10,000 high impact journals are given Journal Impact Factors which are listed each year in the Journal Citation Reports – the JIF is calculated as the ratio of the journal’s citation impact to the volume of research papers it publishes. Millions of researchers are incentivised to publish in ‘Impact Factor journals’ and ambitious scholars are easily enticed into sending their manuscripts to journals that prominently display their Impact Factor. The problem here is that many questionable journals state that they are indexed in such databases when they’re not. Or they announce their ‘Impact Factor’ even when it has not been provided by Clarivate Analytics (formerly ISI and Thomson Reuters), the owner of the Journal Citation Reports and provider of the Journal Impact Factor. Most young academics don’t realise that many of these questions can easily be checked online:

Is the journal indexed in Web of Science?

Is the journal indexed in Scopus?

Is the journal indexed in Medline?

Likewise, once an article has been published in a journal, it is easy to check that the publisher has deposited the digital object identifiers (DOIs) in the Crossref database. Once the DOI has been correctly deposited, then it officially exists and people all over the world can find the article through search engines like Google Scholar and Microsoft Academic, and even more importantly they can accurately cite it pointing fellow academics to the DOI link. Again, a quick check for DOIs is freely available here:

Is this DOI deposited in the Crossref database?

Open Access

The frustration of the academic community by rising subscription prices and a feeling of having to pay twice when research has been funded by public money and then published behind a subscription wall led to the open access movement by which the reader pays no charge to access the results. However, once an article is accepted, the author is usually asked to pay an article processing (or publishing) charge (APC) which often costs hundreds, and can easily run into thousands of dollars, a fee which in many developing countries is covered by the researchers themselves. Under pressure to publish and with little guidance on journal choice, some academics are falling prey to unscrupulous publishers who charge APCs but do not provide a professional publishing service, these have been termed ‘predatory publishers’.

Predatory publishing

Such publishers may exaggerate or misrepresent their services by claiming to be based in a traditional publishing hub while hiding their real location, claiming to provide rigorous peer review but publishing far too quickly for that to be possible or presenting editorial boards of academics who do not know or agree to be listed. Defining a publisher or publication as ‘predatory’ however, is no simple matter and sometimes there is a fine line between acceptable and unacceptable behaviour, e.g. at what point do repeated calls for papers become ‘spam’? Some publishers have found their journals on a predatory publishers blacklist while at the same time being indexed in one of the prestigious databases assumed to be whitelists. One university librarian, Jeffrey Beall maintained a list of ‘probable, possible and potential predatory publishers’ since 2008 (no longer available) and which most recently listed more than 12,000 titles and publishers each included for questionable publication practice based on a list of over 50 criteria.

There is no universally agreed definition of a predatory journal or publisher, indeed nor is there a standard for a ‘high quality journal’. Most people who provide advice on identifying predatory journals start by warning people to watch out for spelling mistakes, typos and grammatical errors on a journal’s website or submission instructions. But equating imperfect English with questionable publication ethics in regions where millions of non-native English speakers are engaged in education and research is itself, an assumption that should be taken in context. Native-level English should not be a pre-requisite for publishing quality research in quality journals, there must be other ways to ensure safe submission of manuscripts and evaluation of journals and publishers.

The Committee on Publication Ethics (COPE) celebrates its 20th anniversary this year and now boasts more than 10,000 members. It has produced a code of conduct and a range of guidelines for authors, editors and peer reviewers. Most serious publishers now adhere to the COPE Code of Conduct and guidelines and this is one of the first things authors should check for.

Think, Check, Submit

Researchers need to be routinely trained on how to conduct a rudimentary evaluation of a journal. They need to be trained on what to look for and what are the tell-tale signs that should set alarm bells ringing. So, what can the busy researcher do to distinguish good journals from bad?

Several international publishing associations have pooled their resources and launched the Think. Check. Submit. campaign – this was launched during the 2015 meeting of the Association of Learned and Professional Society Publishers, ALPSP. It leads the researcher through the three main steps and includes a check list for researchers to look through before they submit their manuscript to any journal. In the Arab region, we believe that following the Think. Check. Submit. campaign will help the regional research community avoid these pitfalls and publish safely, to view the initiative click here:

Think. Check. Submit: http://thinkchecksubmit.org/

Think. Check. Submit (Arabic): http://knowledgee.com/thinkchecksubmit-ar/

This post was first published on the KnE Blog on 28 February 2017.

Keeping pace with changes in eJournal technology

Tracy Gardner: keeping pace with eJournal technology

eJournal technology is an essential part of the scholarly publishing industry. It is also the topic of one of our most popular training courses. Here, we spoke to Understanding eJournal Technology co-tutor, Tracy Gardner, about the challenges of keeping up-to-date in this area.

SK: What is the main challenge that publishers face in the field?
TG: The pace of change within eJournals technology is fast. This technology has removed the barriers between production, editorial, marketing, sales, customer services and most importantly – the customers. Renew Training started running business technology courses specifically for publishers around 7 years ago and during all that time the same course has never been delivered twice!

SK: What is driving the pace of change?
TG: Changes in how libraries authenticate their patrons, how they manage reader navigation and the implementation of new search and discovery tools has changed the eJournal landscape dramatically.

SK: Who does this affect?
TG: For those in sales, marketing and customer service it can be hard to understand the business ramifications of how eJournal technology affects the way librarians and researchers find and access content. How does the fact a library uses a proxy, or only has one IP address for their entire institution, or indeed if their IP addresses are a state secret impact how researchers read your content? Does Shibboleth or Athens solves these issues, or does it create news ones? What about OpenURLs and working with link resolvers – and what are resource discovery services and tools and why should you worry about them?

For those in operational or technology roles, the business technology side of eJournals can seem daunting and especially for those new to the industry, the way the information community works can seems counter to the way many other business sectors operate.

SK: How can you keep pace of these changes?
TG: Educate those in sales, marketing, customer services, product development, editorial, project management and IT in the technologies. These roles are all vital to the delivery of eJournals. You need to clearly position these technologies in the context of the industry issues they aim to solve so your teams understand how they are used throughout the supply chain internally and by librarians through to end users. Understand a) your customers' technical and business requirements, and b) how technology plays a role in discoverability and deploying eJournals.

Tracy Gardner has over 17 years’ experience in marketing and communications and has worked for CatchWord, Ingenta, CABI Publishing and Scholarly Information Strategies. Her career has focussed on improving communication channels between publishers, intermediaries and librarians and she understands the business of scholarly publishing from many different perspectives.

Tracy is co-tutor with Simon Inger on Understanding eJournal Technology course run by ALPSP in association with Renew Training. If you are flummoxed by any of the above terminology, or if you would like to understand more about how your customers are using business technology to serve their patrons, then come along to the next course on 13 November 2013 in Oxford.

How do you make your publication stand out from the crowd? Julia Lampam reflects...

Julia Lampam: make your publication stand out

'How do you make your publication stand out from the crowd? What tools can you use to publicise a journal article? What can you do to harness the immense power of social media to increase awareness of your content?

These questions and more are raised by publicists, marketers, editors and authors alike as we strive to improve the discoverability of the rich academic content we publish. And why? Because we’re all aiming to increase the discoverability and visibility of an article through a number of metrics and citations, with the impact factor being the most widely used.

It's all about discoverability and visibility on an article level
During our forthcoming course, Getting the Most from Journal Publicity, Alexa Dugan and I will share our experience of maximising the promotional and marketing resources available to extend the reach and impact of the research in your publications.

Publicity by its very nature is unpredictable. 
But by asking yourselves a pertinent set of questions and armed with a handful of tools, you can develop and instigate a proactive media campaign to draw attention to the research. By taking advantage of social media and online networks, as well as traditional PR resources, article level publicity efforts can help you reach wider audiences, increasing web traffic to the content and thereby potentially improving the number of citations.

What works, and what doesn't?
The evaluation of such initiatives plays just as an important role as planning – knowing what works and what doesn’t will enable you to focus on which articles you can target your limited means. Publicity campaigns take time and resource, with some being more effective than others. In addition, there is an on-going debate about how to measure the return on investment on such activity. You can focus on the number of citations, journal impact factors, web traffic to an article, number of downloads but you should also think of other benefits such as attracting key authors, as well as developing and strengthening the relationships between publisher and their communities.

Be part of the conversation
The most successful campaigns enable research to embed itself into extended communities of interest and become part of the conversation. I recall working on a journal article publicity campaign about research into the best way to cook your vegetables … two weeks later I read about the research in the weekly musings from my veg box provider … the campaign had gone full circle! Of course this doesn’t happen every time, but when it does; you certainly get a buzz from instigating a successful media campaign.'

Julia Lampam is responsible for Wiley's corporate communications and book fairs within Europe, the Middle East and Asia, and co-chairs the company's global social media group. Previously she managed their publicity activities, instigating proactive PR strategies for academic journals and the For Dummies and Frommer's brands; as well as launching Wiley’s online newsroom.

Julia is co-tutor on Getting the Most from Journal Publicity with Alexa Dugan. Book your place now.

Is the journal brand dead? Marketing in an open access world

Tim Redding, Nature Publishing, talks journal brands

In November, ALPSP held one of our most successful seminars in 2012 - Beyond the Rhetoric: New opportunities in open access. Tim Redding, Head of Marketing for BioPharma, Life and Physical Sciences at Nature Publishing provided some insights into branding.

He articulated access to research is universal  and it is the top tier journals with large circulations that have lost out. With all journals, whatever their tier, you now have to woo authors. The circulation argument no longer works. There are a number of factors that need to be taken care of when considering your organisation or journal brand.

Article level metrics are vital. Ideally you will have a metrics button on each article. You need to focus on service: from time to publication through to ease of submission and discoverability. Reviewers and editorial boards are advocates for the journal. They are just as key as authors, so treat them accordingly. Happy reviewers are needed for rapid publication and to meet authors' service level expectations. Deal with them fairly and efficiently and consider recognition of their contribution. Frontiers puts reviewer names on papers giving more credit to what the reviewers are contributing to the scientific process. Common courtesy doesn't go amiss: send thank you letters and acknowledgements.

Redding also outlined the difficulties with hybrid titles. You have to consider transparency of amount of content that is paid for and ensure you have fair pricing. On the flip side, you need to be clear about cost per download or cost per local citation. Ensure your business model is more fluid than before and consultation and transparency with libraries is paramount.

There are particular challenges with visibility. How can you get papers seen in mega journals? How do you ensure standout and how do authors reach outside their niche? Papers are seen if there is a network for them, regardless of how interesting or quirky they are.

Tools to use for visibility should include email. It is still powerful, if used wisely. Content marketing is good for authors and helps define the journal. Give authors tools to help themselves e.g. sharing boxes and social tools. Empower the author to promote their paper. Give them an email template and make it easy for them to share.

Unsurprisingly, Redding is a big advocate of using social media.  They have the following number of accounts for science engagement at Nature:

• 40 Twitter
• 24 Facebook
• 8 blogs
• 6 MySpace
• 8 LinkedIn

Social media provides tools for visibility. They received 120,000 'Likes' on Facebook for nature.com. As a network, Facebook can be the second largest referrer after Google. While it is a forum for engagement and comment, you need to keep an eye on it and actally engage, so don't just pop it up there and forget about it.

Social media works best when marketing (key messages, sales) and editorial (credibility) work together. It allows you to gain feedback and insight into your authors and readers. While audience can be vocal, you can turn this to your advantage by embracing it, and not ignoring it. With Twitter, autofeeds work, but nothing compares to editorial engagement.

Infographics: here's one he prepared earlier

But what kind of content works best? Pictures and video can help you and increase interaction on Facebook. This type of content encourages sharing which can go viral. Infographics can help to explain complex information and can help your content standout from the clutter. Good content can act as a talking point.

Paid search is worth considering as it is useful to grow audience quickly and cost effectively - particularly before indexing. Facebook drives page likes, Google AdWords is good for directing traffic and StumbleUpon is less than $0.10 per click. Also consider Reddit, Digg and LinkedIn.

Tracking can be difficult as there is no direct correlation, unlike subscriptions. But by tracking submission rate against marketing campaigns, you can show trends, albeit with a time lag. A guide to authors page views is also a good indicator of interest.

All these techniques form part of a long game. Build your brand and build your registrations; build web traffic and submissions will come. Use author marketing to full effect: survey all authors to find out why they submitted to your journal. This will not only help you define your brand, but will also provide good insight into your service levels as they are part of the author/academic/research community's most critical touch point with your brand.

Walter Landor, the father of modern branding, stated that brand is not just a name and logo, it has evolved. It is not just company telling you what the product is. Customers define brand just as much as company. Is the journal brand dead? Are journal brands still relevant? Why don't researchers just publish on WordPress? Redding believes it is about trust, reach and discoverability:

• brands give trust and authority and quickly allow you to identify content you need
• brands help authors ensure that the audience reading their research is the right one and valued
• brands give papers Google juice and discoverability.

He closed by saying in an online open access world, brands are still critical and far from dead. Long live the journal brand.