Scholarly HTML would be nice, but...

I'm quite interested in the idea of Scholarly HTML, as espoused in Pete Sefton's blog, and I've commented on some of Peter Murray Rust's hamburger PDF comments previously (although I do think a lot of people confuse wild PDF with well-made, should one say Scholarly PDF). I've always been slightly worried by one thing though.

A well-known advantage of PDF is that it pretty much assures I can save a document, share it, move it around etc and it will still be intact and readable. That's one of the reasons it's so popular.

Mostly we don't do that with HTML. Mostly we just point to it. But if I see an article these days, I want it on my computer if I'm allowed; this let's me study it at leisure, drop it in my Mendeley system, etc. As pointed out, that works a treat with PDF, and pretty well with Word or OpenOffice documents as well. This applies even where the document is quite heavily compound, with many embedded images, tables etc.

But if I try saving a HTML document to my hard disk, nothing very standard happens. OK, if I use Safari on my Mac, I get a .webarchive file, which is quite nice as I can do all the things with it that I could do with a PDF and Word etc, and when I open it later it will be as it was before, with all the images in place. But neither IE nor Firefox seem capable of opening a .webarchive file.

If I try saving the same article from Firefox, I get a .html file with the main article in it, and a directory with associated files in it (eg images). Safari does seem capable of opening this combination, but it's pretty ugly, and hard to move around. I haven't tried IE as I don't have easy access to it.

Is there in existence or development a standard approach to packaging the HTML and associated files that would be as convenient as the .webarchive, but usable across all browsers? If so, Scholarly HTML would be that little bit closer!

More activity on semantic publishing

If you saw tweets from @cardcc today, you might realise I’ve been very interested in a couple of recent developments in semantic publishing. I wrote earlier about linking data to journal articles, including David Shotton’s adventures in semantic publishing. David’s work was one of those included in the review article in the Biochemical Journal by Attwod, Kell, McDermott et al (2009). The article ranged over the place of ontologies and databases, science blogs, and various experiments. These included

• RSC and Project Prospect,
• The ChemSpider Journal of Chemistry,
• The FEBS Letters experiment,
• PubMed Central and BioLit,
• Shotton’s PLoS experiment,
• Elsevier Grand Challenge,
• Liquid Publications,
• The semantic Biochemical Journal experiment.

The latter was the real focus of the article, available in PDF, but which if read through a special reader called Utopia Document displayed some active capabilities. These included the ability to visualise and rotate 3-d images of proteins, to see tables represented as graphs (or vice versa) and to link to entries in nucleic acid databases. The capabilities were perhaps a bit awkward to spot and to manipulate, but still interesting. This article is (gold) open access. Other articles in the issue have also been instrumented in this way.

It’s clearly early days for Utopia, and I wasn’t wholly impressed with it as a PDF reader, but I was certainly very excited at some of what I read and saw.

I also read today a very different article (I think not available on open access), by Ruthensteiner and Hess (2008). They describe the processes in making 3-d models of biological specimens, and presenting them in PDF, readable by a standard Acrobat Reader. The 3-d capability was at least as good as if not better than the Utopia results.

Because it’s getting late, I’ll end with my last tweet:

“My head is spinning with semantic article possibilities. I hope some get picked up in new #jiscmrd proposals, see http://www.jisc.ac.uk/fundingopportunities/funding_calls/2009/12/1409researchdata.aspx"

Attwood, T. K., Kell, D. B., McDermott, P., Marsh, J., Pettifer, S. R., Thorne, D., et al. (2009). Calling International Rescue: knowledge lost in literature and data landslide! The Biochemical journal, 424(3), 317-33. doi: 10.1042/BJ20091474.

Ruthensteiner, B., & Hess, M. (2008). Embedding 3D models of biological specimens in PDF publications. Microscopy research and technique, 71(11), 778-86. doi: 10.1002/jemt.20618. Pubmed abstract.

Data and the journal article

I recently had a discussion (billed as a presentation, but it was on such an (ahem) intimate scale that it became a discussion) at Ithaka, the organisation in New York that runs JSTOR, ArtSTOR and Portico. We talked about some of the issues surrounding supporting journal articles better with data. Both research funders and some journals are starting to require researchers/authors to keep and to make available the data that supports the conclusions in their articles. How can they best do this?

It seems to me that there are 4 ways of associating data with an article. The first is through the time-honoured (but not very satisfactory) Supplementary Materials, the second is through citations and references to external data, the third is through databases that are in some way integrated with the article, and the fourth is through data encoded within the article text.

My expectation was that most supplementary materials that included data would actually be in Excel spreadsheets, and a few would be in CSV files, while even fewer would be in domain-specific, science-related encodings. I was quite shocked after a little research to find, at least for the Nature journals I looked at, that nearly all supplementary data were in PDF files, while a few were in Word tables. I don't think I found any that were Excel, let alone CSV. This doesn't do much for data re-usability! As things stand currently, data in a PDF document (eg in tables) will probably need to be extracted by hand copy; possibly by cut and paste followed by extensive hand manipulation.

I would expect that looking away from the generalist journals towards domain-specific titles, would reveal more appropriate formats. However, a ridiculously quick check of Chem-Comm, a Royal Society of Chemistry title, showed supplementary data in PDF even for an "electronically enhanced article (eg Experimental procedures, spectra and characterization data, perhaps not openly accessible...).

There’s a bit of concern in some quarters about journals managing data, particularly that data would disappear behind the pay wall, limiting opportunities for re-use.

What would be ideal? I guess data that are encoded in domain-specific, standardised formats (perhaps supported by ontologies, well-known schemas, and/or open software applications) would be pretty useful. I’ve also got a vague sense of unease about the lack of any standardised approach to describing context, experimental conditions, instrument calibrations, or other critical metadata needed to interpret the data properly. This is a tough area, as we want to reduce the disincentives to deposit as well as increase the chances of successful re-use.

Clearly there are many cases where the data are not appropriate for inclusion as supplementary materials, and should be available by external reference. Such would be the case for genomics data, for example, which must have been deposited in an appropriate database (the journal should demand deposit/accession data before publication).

External data will be fine as long as they are on an accessible (not necessarily open) and reasonably permanent database, data centre or repository somewhere. I do worry that many external datasets will be held on personal web sites. Yes, these can be web-accessible, and Google-indexed, but researchers move, researchers die, and departments reorganise their web presence, which means those links will fail, and the data will disappear (see the nice Book of Trogool article "... and then what?").

Sometimes such external data can be simply linked, eg a parenthetical or foot-noted web link, but I would certainly like to encourage increasing use of proper citations for data. Citations are the currency of academia, and the sooner they accrue for good data, the sooner researchers will start to regard their re-usable data as valuable parts of their output! It’s interesting to see the launch of the DataCite initiative coming up soon in London.

There is this interesting idea of the overlay data journal, which rather turns my last paragraph on its head; the data are the focus and the articles describe the data. Nucleic Acids Research Database Issue articles would be prime examples here in existing practice, although they tend to describe the dataset as a persistent context, rather than as the focus for some discovery. The OJIMS project described a proposed overlay journal in Meteorology; they produced a sample issue and a business analysis, but I’m not sure what happened then.

The best (and possibly only) example I know of the database-as-integral-part-of-article approach is Internet Archaeology, set up in 1996 (by the eLib programme!) as an exemplar for true internet-enabled publishing. 13 years later it's still going strong, but has rarely been emulated. Maybe what it provides does not give real advantages? Maybe it's too risky? Maybe it’s too hard to create such articles? Maybe scholarly publishing is just too blindly conservative? I don't know, but it would be good to explore in new areas.

Peter Murray-Rust has argued eloquently at the tragedy of data trapped and rendered useless in the text, tables and figures of articles. We would like to see articles semantically enriched so that these data can be extracted and processed. Encoded data points us to a few examples, such as the Shotton enhanced article described in Shotton et al 2009, and also to the Murray-Rust/Sefton TheoREM-ICE approach (although that was designed for theses, I think). I think the key here is the lack of authoring tools. It is still rather difficult to actually do this stuff, eg to write an article that contains meaningful semantic content. The Shotton target article was marked up by hand, with support from one of the authors of the W3C SKOS standard, ie an expert! The chemists having been working on tools for their community, both the ICE example, and also MS Chem4Word, maybe ChemMantis, etc.

This last paragraph also points us towards the thesis area; I think this is one that Librarians really ought to be interested in tackling. What is the acceptable modern equivalent to the old (but never really acceptable) practice of tucking disks into a pocket inside the back cover of a thesis? Many universities are now accepting theses in digital form; we need some good practice in how to deal with their associated data.

So, we seem to be quite a way from universal good practice in associating data with our research articles.

Shotton, D., Portwin, K., Klyne, G., & Miles, A. (2009). Adventures in semantic publishing: exemplar semantic enhancements of a research article. PLoS Computational Biology, 5(4). doi: 10.1371/journal.pcbi.1000361.

ARCHER: a component of Australian e-Research infrastructure?

At the e-Science All Hands meeting, David Groenewegen from Monash spoke (PPT, also from Nick Nicholas and Anthony Beitz) about the outputs of the ARCHER project, almost finished, intended to provide tools for e-Research infrastructure. They see these e-Research challenges:

• "Acquiring data from instruments
• Storing and managing large quantities of data
• Processing large quantities of data
• Sharing research resources and work spaces between institutions
• Publishing large datasets and related research artifacts
• Searching and discovering"

The tools they have nearly completed (the project finishes this month) include:

• "ARCHER Research Repository - for storing large datasets, based on SRB
• Distributed Integrated Multi-Sensor & Instrument Middleware – concurrent data capture and analysis
• Scientific Dataset Manager (Web) - for managing datasets
• Metadata Editing Tool
• Scientific Dataset Manager (Desktop) – for managing datasets
• Analysis Workflow Automation Tool - streamlining analysis
• Collaborative Workspace Development Tool - bringing researchers together"

The research repository is based around a simplified version of what they call "CCLRC Scientific metadata", which they said was the only appropriate set of metadata they could find at the time. Here's a simpified diagram:


This does look to me like the metadata for a Current Research Information System (CRIS); I've spoken of these before. Maybe the CERIF metadata might do a similar job? Later we heard that the ANDS programme was to use yet another metadata set or standard (ISO2146); OK guys, I got a bit confused at this point!

Clearly this is a generic system; they also have some customisations coming for crystallographers, including the wonderfully-named TARDIS (The Australian Repositories for Diffraction Images). It's not yet clear to me how domain science curation and domain-specific metadat fit into this model, but I hope to find out more next month.

So where next for ARCHER? David wrote:

• "Currently testing the tools for release by late September
• Some tools already out in the wild and in use
• Expecting that the partners will continue to develop the tools they created
• New enhanced versions already being worked on
• Looking at how these tools might be used within ANDS (Australian National Data Service) & ARCS (Australian Research Collaborative Service) and beyond!"

This does look like good stuff!

(I think ARCHER is a collaboration of ANU, James Cook, Monash and Queensland Universities.)

Negative click repositories

I wanted to write a bit more about this idea of a negative click repository (negative cost was a bad name, as there is a real positive $ and £ cost to the repository, rather than the depositor). First some ancient history...

When I joined the University of Glasgow in 2000, the Archives and Business Records Centre with other collaborators within the University were near the end of a short project on Effective Records Management (ERM, http://www.gla.ac.uk/infostrat/ERM/). During the course of that project, they surveyed committee clerks (who create many authoritative institutional records) on how much effort they were willing to put in, how many clicks they were willing to invest, to create records that would be easily maintainable in the digital era. The answer was: zero, none, nada! Rather than give up at this point, the team went on to create CDocS (http://www.gla.ac.uk/infostrat/ERM/Docs/ERM-Appendix2.pdf), an instrumented addition to MS Word that allowed the committee clerks to create their documents in university standard forms, with agreed metadata, with the documents and metadata automatically converted into XML for preservation and to HTML for display and sharing. ICE (see below) might be a contemporary system of a related kind, in a slightly different area. Thanks to James Currall for updating me on ERM and CDocS.

In April 2007, Peter Murray Rust had an epiphany thinking about repositories on the road to Colorado, realising that SourceForge was a shared repository that he had been using for years, and speculating that it might be used for writing an article. The tool for control of managing versions and sharing in SourceForge is SVN… Peter wrote about the complex workflow in writing a collaborative article, but then wrote:

“BUT using SVN it’s trivial - assuming there is a repository. So we do not speak of an Institutional Repository, but an authoring support environment (ASE or any other meaningless acronym. ) A starts a project in institutional SVN. B joins, so do C, D, E, etc. They all edit the m/s. Everyone sees the latest version. The version sent to the publisher is annotated as such (this is trivial). All subsequent stuff is tracked automatically. When the paper is published, the institution simply liberates the authorised version - the authors don’t even need to be involved. The attractive point of this - over simple deposition - is that the repository supports the whole authoring process.”

Many of those who left comments disagreed that the technology would work directly as suggested, for various reasons. Google Docs was mentioned as an alternative (still flawed). Peter Sefton mentioned ICE (and Murray Rust subsequently visited USQ to work briefly with the ICE team.

You may also remember Caveat Lector’s series of personae representing stakeholders in the repository game at fictional Achaea University, that I reported on before. Ulysses Acqua was her repository manager, and here’s a quote from his attempts to explain the advantages of his repository to faculty; they ask:

“Can it produce CVs or departmental-activity reports automatically? No. Can it be tweaked so that the Basketology collection looks like the Basketology website? No. (The software can do that, in fact, but Ulysses can’t.) Can it talk to campus IT’s file-storage-cum-website servers? No. Can it harvest faculty articles from disciplinary repositories? No. Can it deliver records straight to Achaea Library’s catalogue? No. Can it have access controls per item, such that items are shared with specific people only, with the list controlled by the depositor? No. Can it embargo items, for a certain length of time or indefinitely? No. Can it read a citation, check rights on the journal, and go fetch the paper if rights are cleared? Dream on. Can it restrict items for campus-only access by IP address? No. Does it talk to RefWorks and Zotero and similar bibliographic managers? No. Does it do version control? No.”

The problem here is that the repository adds work, it doesn’t take it away (there are other examples of this in some of the other personae). And overloaded people don’t accept extra work. They may promise to, but they (mostly) don’t do it.

Finally, I posted earlier on Nico Adam’s comments on repositories for scientists. He got stuck, he said: "I had to explain what a repository is from the point of view of functionality - when talking to non-specialist managers, it is the only way one can sell and explain these things…they do not care about the technological perspective…the stuff that’s under the hood. I found it impossible to explain what the value proposal of a repository is and how it differentiates itself in terms of its functionality from, say, the document management systems in their respective companies." It’s worth repeating a couple of extracts from his conclusions:

"Now today it struck me: a repository should be a place where information is (a) collected, preserved and disseminated (b) semantically enriched, (c) on the basis of the semantic enrichment put into a relationship with other repository content to enable knowledge discovery, collaboration and, ultimately, the creation of knowledge spaces. "

And further:

"Now all of the technologies for this are, in principle, in place: we have DSpace, for example, for storage and dissemination, natural language processing systems such as OSCAR3 or parts of speech taggers for entity recognition, RDF to hold the data, OWL and SWRL for reasoning. And, although the example here, was chemistry specific, the same thing should be doable for any other discipline. … Yes it needs to be done in a subject specific manner. Yes, every department should have an embedded informatician to take care of the data structures that are specific for a particular discipline. But the important thing is to just make the damn data do work!"

So we need to develop repositories that make the data work to take human work away: negative click repositories. Or maybe not… (sorry about this). I’m just a bit concerned that we might get a set of monumental edifices built on DSpace or ePrints.org foundations, resulting in “take it or leave” it decisions. Institutional information environments are highly tailored (not always carefully) and at the department level even more eclectic, and things have to fit together. Maybe as Nico was suggesting, what we need is an array of tools, connected together by technologies like Atom/RSS and/or OAI-ORE that can be configured so as to link the components into an information management system that works to reduce the publishing effort on campus, and captures the intellectual product on the way.

People appear to have lots of ideas on what negative click repositories might do. We could have tools for supporting the scientist in their information sharing (web sites, bibliographies and CVs). Tools for shared data management. Tools for shared writing. Tools even for the library to support faculty in dealing with publishers. And of course tools to help management count their beans. I’d like to begin to collect and order these and other suggestions if possible, so please leave comments or tag your blogs with “negative click”…

IJDC again

At the end of July I reported on the second issue of the International Journal of Digital Curation (IJDC), and asked some questions:

"We are aware, by the way, that there is a slight problem with our journal in a presentational sense. Take the article by Graham Pryor, for instance: it contains various representations of survey results presented as bar charts, etc in a PDF file (and we know what some people think about PDF and hamburgers). Unfortunately, the data underlying these charts are not accessible!

"For various reasons, the platform we are using is an early version of the OJS system from the Public Knowledge Project. It's pretty clunky and limiting, and does tend to restrict what we can do. Now that release 2 is out of the way, we will be experimenting with later versions, with an aim to including supplementary data (attached? External?) or embedded data (RDFa? Microformats?) in the future. Our aim is to practice what we may preach, but we aren't there yet."

I didn't get any responses, but over on the eFoundations blog, Andy Powell was taking us to task for only offering PDF:

"Odd though, for a journal that is only ever (as far as I know) intended to be published online, to offer the articles using PDF rather than HTML. Doing so prevents any use of lightweight 'semantic' markup within the articles, such as microformats, and tends to make re-use of the content less easy."

His blog is more widely read than this one, and he attracted 11 comments! The gist of them was that PDF plus HTML (or preferably XML) was the minimum that we should be offering. For example, Chris Leonard [update, not Tom Wilson! See end comments] wrote:

"People like to read printed-out pdfs (over 90% of accesses to the fulltext are of the pdf version) - but machines like to read marked-up text. We also make the xml versions availble for precisely this purpose."

Cornelius Puschmann [update, not Peter Sefton] wrote:

"Yeah, but if you really want semantic markup why not do it right and use XML? The problematic thing with OJS (at least to some extent) is/was that XML article versions are not the basis for the "derived" PDF and HTML, which deal almost purely with visuals. XML is true semantic markup and therefore the best way to store articles in the long term (who knows what formats we'll have 20 years from now?). HTML can clearly never fill that role - it's not its job either. From what I've heard OJS will implement XML (and through it neat things such as OpenOffice editing of articles while they're in the workflow) via Lemon8 in the future."

Bruce D'Arcus [update, not Jeff] says:

"As an academic, I prefer the XHTML + PDF option myself. There are times I just want to quickly view an article in a browser without the hassle of PDF. There are other times I want to print it and read it "on the train."

"With new developments like microformats and RDFa, I'd really like to see a time soon where I can even copy-and-paste content from HTML articles into my manuscripts and have the citation metadata travel with it."

Jeff [update, not Cornelius Puschmann] wrote:

"I was just checking through some OJS-based journals and noticed that several of them are only in PDF. Hmmm, but a few are in HTML and PDF. It has been a couple of years since I've examined OJS but it seems that OJS provides the tools to generate both HTML and PDF, no? Ironically, I was going to do a quick check of the OJS documentation but found that it's mostly only in PDF!

"I suspect if a journal decides not to provide HTML then it has some perceived limitations with HTML. Often, for scholarly journals, that revolves around the lack of pagination. I noticed one OJS-based journal using paragraph numbering but some editors just don't like that and insist on page numbers for citations. Hence, I would be that's why they chose PDF only."

I think in this case we used only PDF because that was all our (old) version of the OJS platform allowed. I certainly wanted HTML as well. As I said before, we're looking into that, and hope to move to a newer version of the platform soon. I'm not sure it has been an issue, but I believe HTML can be tricky for some kinds of articles (Maths used to be a real difficulty, but maybe they've fixed that now).

I think my preference is for XHTML plus PDF, with the authoritative source article in XML. I guess the workflow should be author-source -> XML -> XHTML plus PDF, where author-source is most likely to be MS Word or LaTeX... Perhaps in the NLM DTD (that seems to be the one people are converging towards, and it's the one adopted by a couple of long term archiving platforms)?

But I'm STILL looking for more concrete ideas on how we should co-present data with our articles!

[Update: Peter Sefton pointed out to me in a comment that I had wrongly attributed a quote to him (and by extension, to everyone); the names being below rather than above the comments in Andy's article. My apologies for such a basic error, which also explains why I had such difficulty finding the blog that Peter's actual comment mentions; I was looking in someone else's blog! I have corrected the names above.

In fact Peter's blog entry is very interesting; he mentions the ICE-RS project, which aims to provide a workflow that will generate both PDF and HTML, and also bemoans how inhospitable most repository software is to HTML. He writes:

"It would help for the Open Access community and repository software publishers to help drive the adoption of HTML by making OA repositories first-class web citizens. Why isn't it easy to put HTML into Eprints, DSpace, VITAL and Fez?

"To do our bit, we're planning to integrate ICE with Eprints, DSpace and Fedora later this year building on the outcomes from the SWORD project – when that's done I'll update my papers in the USQ repository, over the Atom Publishing Protocol interface that SWORD is developing."

So thanks again Peter for bringing this basic error to my attention, apologies to you and others I originally mis-quoted, and I look forward to the results of your efforts! End Update]

Supplementary Material in journal publishing

I went to a couple of interesting events in March and April. The first was the eJournal Archiving & Preservation Workshop held at the British Library on 27 March, 2007 (sponsored by the Digital Preservation Coalition, BL and JISC). The keynote was Anne Kenney talking about the "Metes and Bounds" report on eJournal preservation, and there were many good talks. But the interesting thing in this context was how often the problem of "supplementary materials" came up again and again in questions. This meant all sorts of things, including multimedia, but in particular this related to associated data. A good example of a journal that specifically aims to exploit the Internet's capabilities in providing access to supplementary materials (rather than just transporting two-column PDFs around for me to print off) is Internet Archaeology. The problem of course is that this kind of material falls outside the bounds of things that can be easily preserved with the developing preservation systems.

The next event was an ALPSP workshop on the transformation of research communication, on 13 April at the IMechE in London. This event was mainly aimed at publishers, but again supplementary materials and specifically data came up several times in questions and panel sessions, although this time data also came up in presentations as well (eg Christine Borgman and Simon Coles).

Of course, while having a journal literature that enables connection to underlying data is a pretty neat idea, not everyone is happy with the publishers taking control of that data and adding it to their lock-in of scholarly intellectual property. Generally I agree with these concerns, but we have yet to establish a sustainable alternative model for providing continuing access to these data either. I think this one will run and run!