Beyond the PDF – it is time for a workshop

PDF has become the standard way we consume scientific papers, but in fact is not a good format for this purpose at all. Or as Martin Robbins said at the recent Science Online London conferencePDF is an insult to science. The problem was nicely illustrated by Duncan Hull, using a quote from Peter Murray-Rust from a May 2008 article:

Metadata or Meatdata? The PDF "hamburger"...

Flickr image by dullhunk. From his Defrosting the Digital Library slideshow.

There are of course ways journal publishers can add metadata to PDF files, e.g. using XMP markup. But that is only a workaround – what we really want is journal papers in a format that is all about document structure and not about looking good in print. XML is obviously that format with the NLM-DTD as the de facto standard for scholarly publications. Many journal publishers use that format internally, as does PubMed Central for displaying fulltext papers, as well as archiving projects such as Portico.

But there are two problems with how NLM-DTD is used now. The first problem is that most scientific papers still are ultimately read as printouts of PDF files, even though most journals now are online only. I wrote in January that this reading behavior is starting to change (How do you read papers? 2010 will be different), and new article formats – such as the Article of the Future by Cell Press – and the success of the iPad are two major reasons for that.

The second problem is that there are no good NLM-DTD tools for authors. Lemon8-XML and the Microsoft Word Article Authoring Add-In are two examples that I have written about before. Publishers spend a significant amount of time and money (and using tools such as eXtyles) to convert submitted manuscripts from Microsoft Word, Open Office or LaTeX formats into NLM-DTD. I wrote about my paper writing dream machine that would use the NLM-DTD more than two years ago. I still believe that the ideal authoring tool should be web-based, but in 2010 this should be done in HTML5 and not Adobe Flash or Microsoft Silverlight.

The two problems are obviously related. When more people are reading papers in other formats than PDF and see the advantages, it changes the idea of a scientific paper that most people have from a static document do a document that is enriched with primary research data, visualizations that use 3D and video, links to related resources, the possibility to comment, and has more than one document version. In other words, what HTML and the WWW were invented for by Tim Berners-Lee when working at CERN. At this point the incentives to create better authoring tools will be much greater, and the second problem should solve itself. And HTML and related technologies have now evolved to the point where they allow the building of some very attractive authoring tools.

Phil Bourne has written and talked a lot about this problem, including a recent editorial in PLoS Computational Biology (What do I want from the publisher of the future?) and a related SciVee video. He has also been working very hard to organize the Beyond the PDF workshop, to be held in San Diego January 19-21. The workshop website went live last week and is a very good source of information. The goal of the workshop is to identify a set of requirements and to start developing open source code that accelerates moving beyond PDF for scientific papers.

I will of course do everything possible to attend this workshop, but haven’t yet secured funding for the trip. What I hope to contribute to the Beyond the PDF project is a more intelligent use of citations (the following was also posted to the Beyond the PDF discussion group):

Unique Author Identifiers
Unique author identifiers such as ORCID not only are a big help in knowledge discovery (finding other interesting papers, datasets, etc. by the same person), but they can also help to better define the contributions of a researcher to a particular paper. This could mean a general description of the contribution (had idea for project, collected data, helped write manuscript, etc.), or could also describe a very specific contribution (researcher X did experiment Y).

Citation styles
We already have far too many citation styles, but the styles we use
have several important shortcomings. I suggest the following changes:

  • Use the DOI instead of volume and page numbers whenever possible
  • Use ORCID to link to the authors of the citations
  • Use the Citation Typing Ontology (CiTO) to describe the meaning of the citation
  • Use a note field to explain why the citation was used

Any authoring tool should obviously use the Citation Style Language (CSL) to format citations. And the citations should be provided with a CC Zero or similar license to allow reuse.

Cited by
At least as important as the citations by a particular paper are the incoming citations, the works that cite a paper. We need much better mechanisms to automate these “trackbacks”, and this should go beyond other papers and also include datasets, blog posts, etc. The incoming citations are of course very helpful for discovery, and the basis for alternative metrics.

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11 Responses to Beyond the PDF – it is time for a workshop

  1. John Wilkins says:

    All nice in theory, but here’s what will actually happen:

    Journal editors will not understand all this, and will insist on getting final XML documents from authors with the right DTD.

    Authors will try to do this in the usual authoring tools like Werd. They will screw it up, because they are, well, authors not compositors. Their papers will take longer to publish because of the cycles of return and resubmit. Pressure will be put upon the journal editor, who will pressure the publishers, who will go back to what they already know.

    Microsoft will create a plugin that is more or less compliant for authoring to the NLM DTD (or some other DTD), but, being Microsoft, will add all kinds of useless garbage, sorry, features that make using their post processor mandatory.

    It will not work well. It will exclude all non-Windows users. It will generate a horrible looking page that will need to be post processed to remove all the MS-specific code.

    The problem with all markup language solutions is the lack of a decent editor that is cross-platform, validates, and is easy to use (i.e., doesn’t require that the author be a compositor), and what is more, this has been the problem since the US DoD mandated it for all contract proposals back in the 1980s.

  2. Martin Fenner says:

    John, thank you for your reality check. You are of course right that changing the tools for publishing a paper will only work if they make it easier and not more difficult for the author. It is already bad enough what we have to do now in order to submit a manuscript (page layout, image editing, reference checking, etc.). Microsoft has released a Microsoft Word plugin that creates NLD-DTD compliant XML in 2008, and it indeed only works for the Windows version.

    For these reasons – and the fact that most publications are collaborative efforts – I firmly believe that the next generation of authoring tools will be web-based. And that they will not be based on Google Docs, which still looks very much like a desktop word processor. WordPress might actually be a better starting point to build such an authoring tool.

  3. Duncan Hull says:

    Hi Martin, interesting stuff: wordpress for papers, now that would be nice!

    You said “Use the DOI instead of volume and page numbers” – this might be a bit extreme. I think the DOI is similar to zip/postal codes in this respect. Just like a zipcode can act as a confirmation that the human-readable postal address is correct (and vice versa) so too a DOI confirms that the published metadata is correct too.

    DOI’s aren’t immune to typos and other mistakes, so I think we’ll never be able to rely on them completely – though I’d agree with you that more people should use them by default for referencing and citation.

  4. Martin Fenner says:

    Duncan, I’m not the first to think about WordPress for papers. Phil Lord has a JISC-funded project (Knowledge Blog) working on this.

    Typos will always be a problem with both DOIs and page numbers – Christian Specht recently did a nice analysis of this in the Scientist. I think that author names, title and journal can be used to confirm that the citation is correct.

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  7. Would you propose using DOIs in text citations? I think seeing author-year in text is quite important, since it gives the citation a context: I don’t need to go to the reference list to see who the citation came from. If it’s a colleague, or an author otherwise familiar to me, I can just keep reading.

    Over a few years I might be able to recognize DOIs in the same way, but it might be decades instead of two or three ;)

  8. Martin Fenner says:

    I would use the DOI only in the reference. In the text author-year indeed works much better.

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