Semantic publishing o ers the promise of computable papers, enriched visualisation and a realisation of the linked data ideal. In reality, however, the publication process contrives to prevent richer semantics while culminating in a `lumpen' PDF. In this paper, we discuss a web- rst approach to publication, and describe a three-tiered approach which integrates with the existing authoring tooling. Critically, although it adds limited semantics, it does provide value to all the participants in the process: the author, the reader and the machine.
The publishing of both data and narratives on those data are changing radically.
Linked Open Data and related semantic technologies allow for semantic
publishing of data. We still need, however, to publish the narratives on that data and
that style of publishing is in the process of change; one of those changes is the
incorporation of semantics [
The reality, however, is somewhat di erent. There are signi cant barriers to
the acceptance of semantic publishing as a standard mechanism for academic
publishing. The web was invented around 1990 as a light-weight mechanism for
publication of documents. It has subsequently had a massive impact on society
in general. It has, however, barely touched most scienti c publishing; while most
journals have a website, the publication process still revolves around the
generation of papers, moving from Microsoft Word or LATEX [
In this paper, we describe our attempts to take a commodity publication environment, and modify it to bring in some of the formality required from academic publishing. We illustrate this with three exemplars - di erent kinds of knowledge that we wish to enhance. In the process, we add a small amount of semantics to the nished articles. Our key constraint is the desire to add value for all the human participants. Both authors and readers should see and recognise additional value, with the semantics a useful or necessary byproduct of the process, rather than the primary motivation. We characterise this process as our \three steps to heaven", namely: { make life better for the machine to { make life better for the author to { make life better for the reader
While requiring additional value for all of these participants is hard, and places signi cant limitations on the level of semantics that can be achieved, we believe, it does increase the likelihood that content will be generated in the rst place, and represents an attempt to enable semantic publishing in a real-world work ow. 2
The knowledgeblog project stemmed from the desire for a book describing the
many aspects of ontology development, from the underlying formal semantics, to
the practical technology layer and, nally, through to the knowledge domain [
This contrasts starkly with the web- rst publication process that has become
known as blogging. With any of a number of ready made platforms, it is possible
for authors with little or no technical skill, to publish content to the web with
ease. For knowledgeblog (\kblog"), we have taken one blogging engine,
WordPress [
As well as delivering content, we are also using this framework to investigate semantic academic publishing, investigating how we can enhance the machine interpretability of the nal paper, while living within the key constraint of making
life (slightly) better for machine, author and reader without adding complexity for the human participants.
Scienti c authors are relatively conservative. Most of them have well-established toolsets and work ows which they are relatively unwilling to change. For instance, within the kblog project, we have used workshops to start the process of content generation. For our initial meeting, we gave little guidance on authoring process to authors, as a result of which most attempted to use WordPress directly for authoring. The WordPress editing environment is, however, web-based, and was originally designed for editing short, non-technical articles. It appeared to not work well for most scientists.
The requirements that authors have for such `scienti c' articles are manifold.
Many wish to be able to author while o ine (particularly on trains or planes).
Almost all scienti c papers are multi-author, and some degree of collaboration
is required. Many scientists in the life sciences wish to author in Word because
grant bodies and journals often produce templates as Word documents. Many
wish to use LATEX, because its idiomatic approach to programming documents
is unreplicable with anything else. Fortunately, it is possible to induce
WordPress to accept content from many di erent authoring tools, including Word
and LATEX[
As a result, during the kblog project, we have seem many di erent work ows in use, often highly idiosyncratic in nature. These include: Word/Email: Many authors write using MS Word and collaborate by emailing les around. This method has a low barrier to entry, but requires signi cant social processes to prevent con icting versions, particularly as the number of authors increases.
Word/Dropbox: For the taverna kblog, authors wrote in Word and collaborated with Dropbox.4 This method works reasonably well where many authors are involved; Dropbox detects con icts, although cannot prevent or merge them.
Asciidoc/Dropbox: Used by the authors of this paper. Asciidoc5 is relatively simple, somewhat programmable and accessible. Unlike LATEX which can be induced to produce HTML with e ort, asciidoc is designed to do so.
Of these three approaches probably the Word/Dropbox combination is the the most generally used.
From the readers perspective, a decision that we have made within knowledgeblog is to be \HTML- rst". The initial reasons for this were entirely practical; supporting multiple toolsets is hard, particularly if any degree of consistency is to be maintained; the generation of the HTML is at least partly controlled by the middleware { WordPress in kblog's case. As well as enabling consistency of presentation it also, potentially, allows us to add additional knowledge; it makes semantic publication a possibility. However, we are aware that knowledgeblog currently scores rather badly on what we describe as the \bath-tub test"; while
exporting to PDF or printing out is possible, the presentation is not as \neat" as would be ideal. In this regard (and we hope only in this regard), the knowledgeblog experience is limited. However, increasingly, readers are happy and capable of interacting with material on the web, without print outs.
From this background and aim, we have drawn the following requirements: 1. The author can, as much as possible, remain within familiar authoring environments; 2. The representation of the published work should remain extensible to, for instance, semantic enhancements; 3. The author and reader should be able to have the amount of \formal" academic publishing they need; 4. Support for semantic publishing should be gradual and o er advantages for author and reader at all stages.
We describe how we have achieved this with three exemplars, two of which are relatively general in use, and one more speci c to biology. In each case, we have taken a slightly di erent approach, but have ful lled our primary aim of making life better for machine, author and reader. 3
The representation of mathematics is a common need in academic literature. Mathematical notation has grown from a requirement for a syntax which is highly expressive and relatively easy to write. It presents speci c challenges because of its complexity, the di culty of authoring and the di culty of rendering, away from the chalk board that is its natural home.
Support for mathematics has had a signi cant impact on academic
publishing. It was, for example, the original motivation behind the development of
TEX [
Authors write their mathematics directly as TEX using one of the four markup syntaxes. The most explicit (and therefore least likely to happen accidentally) is through the use of \shortcodes".6 These are a HTML-like markup originating from some forum/bulletin board systems. In this form an equation would be entered as [latex]e=mc^2[/latex], which would be rendered as \e = mc2". It is also possible to three other syntaxes which are closer to math-mode in TEX: $$e=mc^2$$, $latex e=mc^2$, or \[e=mc^2\].
From the authorial perspective, we have added signi cant value, as it is possible to use a variety of syntaxes, which are independent of the authoring engine. For example, a TEX-loving mathematician working with a Word-using biologist can still set their equations using TEX syntax; although Word will not render these at authoring time but, in practice, this causes few problems for such authors, who are experiened at reading TEX. Within an LATEX work ow equations will be renderable both locally with source compiled to PDF, and published to WordPress.
There is also a W3C recommendation, MathML for the representation and presentation of mathematics. The kblog environment also supports this. In this case, the equivalent source appears as follows: <math> <mrow> <mi>E</mi> <mo>=</mo> <mrow> <mi>m</mi> <msup> <mi>c</mi> <mn>2</mn> </msup> </mrow> </mrow> </math>
One problem with the MathML representation is obvious: it is very longwinded. A second issue, however, is that it is hard to integrate with existing work ows; most of the publication work ows we have seen in use will on recognising an angle bracket turn it into the equivalent HTML entity. For some workows (LATEX, asciidoc) it is possible, although not easy, to prevent this within the native syntax.
It is also possible to convert from Word's native OMML (\equation editor") XML representation to MathML, although this does not integrate with Word's native blog publication work ow. Ironically, it is because MathML shares an XML based syntax with the nal presentation format (HTML) that the problem arises. The shortcode syntax, for example, passes straight-through most of the publication frameworks to be consumed by the middleware. From a pragmatic point of view, therefore, supporting shortcodes and TEX-like syntaxes has considerable advantages.
For the reader, the use of mathjax-latex has signi cant advantages. The default mechanism within WordPress uses a math-mode like syntax $latex e=mc^2$. This is rendered using a TEX engine into an image which is then incorporated and linked using normal HTML capabilities. This representation is opaque and non-semantic; it has signi cant limitations for the reader. The images are not scalable { zooming in cases severe pixalation; the background to the mathematics is coloured inside the image, so does not necessarily re ect the local style.
Kblog, however, uses the MathJax library[
Our use of MathJax provides no signi cant disadvantages to the middleware layers. It is implemented in JavaScript and runs in most environments. Although, the library is fairly large (>100Mb), but is available on a CDN so need not stress server storage space. Most of this space comes from the bit-mapped fonts which are only downloaded on-demand, so should not stress web clients either. It also obviates the need for a TEX installation which wp-latex may require (although this plugin can use an external server also).
At face value, mathjax-latex necessarily adds very little semantics to the maths embedded within documents. The maths could be represented as $$E=mc^2$$, \(E=mc^2\)] or <math> <mrow> <mi>E</mi> <mo>=</mo> <mrow> <mi>m</mi> <msup> <mi>c</mi><mn>2</mn> </msup> </mrow> </mrow> </math>
So, we have a heterogenous representation for identical knowledge. However, in practice, the situation is much better than this. The author of the work created these equation and has then read them, transformed by MathJax into a rendered form. If MathJax has failed to translate them correctly, in line with the author's intention, or if it has had some implications for the text in addition to setting the intended equations (if the TEX style markup appears accidentally elsewhere in the document), the author is likely to have seen this and xed the problem. Someone wishing, for example, to extract all the mathematics as MathML from these documents computationally, therefore, knows: { that the document contains maths as it imports MathJax { that MathJax is capable of identifying this maths correctly { that equations can be transformed to MathML using MathJax7.
So, while our publication environment does not result directly in lower level of semantic heterogeneity, it does provide the data and the tools to enable the computational agent to make this transformation. While this is imperfect, it should help somewhat.
In short, we provide a practical mechanism to identify text containing mathematics and a mechanism to transform this to a single, standardised representation. 7 This is assuming MathJax works correctly in general. The authors and readers are checking the rendered representation. It is possible that an equation would render correctly on screen, but be rendered to MathML inaccurately
We do not yet support LATEX/BibTeX citations, although we see no reason why a similar style le should not be supported. We do, however, support BibTeX-formatted les: the rst author's preferred editing/citation environment is based around these with Emacs, RefTeX, and asciidoc. While this is undoubtedly a rather niche authoring environment, the (slightly elided) code for supporting this demonstrates the relative ease with which tool chains can be induced to support kcite: 8 http://wordpress.org/extend/plugins/kcite/ 9 http://wordpress.org/extend/plugins/kcite/ 10 http://www.datacite.org/ 11 http://www.ncbi.nlm.nih.gov/pubmed/ 12 http://arxiv.org/ (defadvice reftex-format-citation (around phil-asciidoc-around activate) (if phil-reftex-citation-override
(setq ad-return-value (phil-reftex-format-citation entry format)) ad-do-it)) (defun phil-reftex-format-citation( entry format ) (let ((doi (reftex-get-bib-field "doi" entry)))
(format "pass:[[cite source='doi'\\]%s[/cite\\]]" doi)))
The key decision with kcite from the authorial perspective is to ignore the reference list itself and focus only on in-text citations, using public identi ers to references. This simpli es the tool integration process enormously, as this is the only data that needs to pass from the author's bibliographic database onward. The key advantage for authors here is two-fold: they are not required to populate their reference metadata for themselves, and this metadata will update if it changes. Secondly, the identi ers are checked; if they are wrong, the authors will see this straightforwardly as the entire reference will be wrong. Adding DOIs or other identi ers moves from becoming a burden for the author to becoming a speci c advantage.
While supporting multiple forms of reference identi er (CrossRef DOI, DataCite DOI, arXiv and PubMed ID) provides a clear advantage to the author, it comes at considerable cost. While it is possible to get metadata about papers from all of these sources, there is little commonality between them. Moreover, resolving this metadata requires one outgoing HTTP request13 per reference, which browser security might or might not allow.
So, while the presentation of mathematics is performed largely on the client, for reference lists the kcite plugin performs metadata resolution and data integration on the server. A caching functionality is provided, storing this metadata in the WordPress database. The bibliographic metadata is nally transferred to the client encoded as JSON, using asynchronous call-backs to the server.
Finally, this JSON is rendered using the citeproc-js library on the client. In our experience, this performs well, adding to the readers' experience; in-text citations are initially shown as hyperlinks; rendering is rapid, even on aging hardware, and nally in-text citations are linked both to the bibliography and directly through to the external source. Currently, the format of the reference list is xed, however, citeproc-js is a generalised reference processor, driven using CSL14. This makes it straight-forward to change citation format, at the option of the reader, rather than the author or publisher. Both the in-text citation and bibliography support outgoing links direct to the underlying resources15. As these links have been used to gather metadata, they are likely to be correct. While these advantages are relatively small currently, we believe that the use of JavaScript rendering over a linked references can be used to add further reader value in future. 13 In practice, it is often more; DOI requests, for instance, use 303 redirects. 14 http://citationstyles.org/ 15 Where the identi er allows { PubMed IDs redirect to PubMed.
For the computational agent wishing to consume bibliographic information, we have added signi cant value compared to the pre-formatted HTML reference list. First, all the information required to render the citation is present in the in-text citation next to the text that the authors intended. A computational agent can, therefore, ignore the bibliography list itself entirely. These primary identi ers are, again, likely to be correct because the authors now need them to be correct for their own bene t.
Should the computational agent wish, the (denormalised) bibliographic data used to render the bibliography is actually available, present in the underlying HTML as a JSON string. This is represented in a homogeneous format, although, of course, represents our (kcite's) intepretation of the primary data.
A nal, and subtle, advantage of kcite is that the authors can only use public metadata, and not their own. If they use the correct primary identi er, and still get an incorrect reference, it follows that the public metadata must be incorrect16. Authors and readers therefore must ask the metadata providers to x their metadata to the bene t of all. This form of data linking, therefore, can even help those who are not using it. 4.1
Microarray Data
Many publications require that papers discussing microarray experiments lodge
their data in a publically available resource such as ArrayExpress [
For the knowledgeblog-arrayexpress plugin,17 therefore, we have again used a shortcode representation, but allowed the author to automatically ll metadata, direct from ArrayExpress. So a tag such as: [aexp id="E-MEXP-1551"]species[/aexp] will be replaced with Saccharomyces cerevisiae, while: [aexp id="E-MEXP-1551"]releasedate[/aexp] will be replaced by \2010-02-24". While the advantage here is small, it is signi cant. Hyperlinks to ArrayExpress are automatic, authors no longer need to look up detailed metadata. For metadata which authors are likely to know anyway (such as Species), the automatic lookup operates as a check that their ArrayExpress ID is correct. As with references 6, the use of an identi er becomes an advantage rather than a burden to the authors.
Currently, for the reader there is less signi cant advantage at the moment. While there is some value to the author of the added correctness stemming from the ArrayExpress identi er. However, knowledgeblog-arrayexpress is currently under-developed, and the added semantics that is now present could be used 16 Or, we acknowledge, that kcite is broken! 17 http://knowledgeblog.org/knowledgeblog-arrayexpress more extensively. The unambiguous knowledge that: [aexp id="E-MEXP-1551"]species[/aexp] represents a species would allow us, for example, to link to the NCBI taxonomy database.18
Likewise, advantage for the computational agent from knowledgeblog-arrayexpress is currently limited; the identi ers are clearly marked up, and as the authors now care about them, they are likely to be correct. Again, however, knowledgeblog-arrayexpress is currently under developed for the computational agent. The knowledge that is extracted from ArrayExpress could be presented within the HTML generated by knowledgeblog-arrayexpress, whether or not it is displayed to the reader for, essentially no cost. By having an underlying shortcode representation, if we choose to add this functionality to knowledgeblogarrayexpress, any posts written using it would automatically update their HTML. For the text-mining bioinformatician, even the ability to unambiguously determine that a paper described or used a data set relating to a speci c species using standardised nomenclature19 would be a considerable boon. 5
Our approach to semantic enrichment of articles is a measured and evolutionary approach. We are investigating how we can increase the amount of knowledge in academic articles presented in a computationally accessible form. However, we are doing so in an environment which does not require all the di erent aspects of authoring and publishing to be over-turned. More over, we have followed a strong principle of semantic enhancement which o ers advantages to both reader and author immediately. So, adding references as a DOI, or other identi er, `automagically' produces an in text citation and a nicely formatted reference list: that the reference list is no longer present in the article, but is a visualisation over linked data; that the article itself has become a rst class citizen of this linked data environment is a happy by-product.
This approach, however, also has disadvantages. There are a number of semantic enhancements which we could make straight-forwardly to the knowledgeblog environment that we have not; the principles that we have adopted requires signi cant compromise. We o er here two examples.
First, there has been signi cant work by others on CiTO [
Second, our presentation of mathematics could be modi ed to automatically generate MathML from any included TEX markup. The transformation could be performed on the server, using MathJax; MathML would still be rendered on the client to webfonts. This would mean that any embedded maths would be discoverable because of the existence of MathML, which is a considerable advantage. However, neither the reader nor the author gain any advantage from doing this, while paying the cost of the slower load times and higher server load that would result from running JavaScript on the server. More over, they would pay this cost regardless of whether their content were actually being consumed computationally. As the situation now stands, the computational user needs to identify the insert of MathJax into the web page, and then transform the page using this library, none of which is standard. This is clearly a serious compromise, but we feel a necessary one.
Our support for microarrays o ers the possibility of the most speci c and increased level of semantics of all of our plugins. Knowledge about a species or a microarray experimental design can be very prescisely represented. However, almost by de nition, this form of knowledge is fairly niche and only likely to be of relevance to a small community. However, we do note that the knowledgeblog process based around commodity technology does o er a publishing process that can be adapted, extended and specialised in this way relatively easily. Ultimately the many small communities that make up the long-tail of scienti c publishing adds up to one large one. 6
Semantic publishing is a desirable goal, but goals need to be realistic and achievable. to move towards semantic publishing in kblog, we have tried to put in place an approach that gives bene t to readers, authors and computational interpretation. As a result, at this stage, we have light semantic publishing, but with small, but de nite bene ts for all.
Semantics give meaning to entities. In kblog, we have sought bene t by \saying" within the kblog environment that entity x is either maths, a citation or a microarray data entity reference. This is su cient for the kblog infra-structure to \know what to do" with the entity in question. Knowing that some publishable entity is a \lump" of maths tells the infra-structure how to handle that entity: the reader has bene t from it looking like maths; the author has bene t by not having to do very much; and the infra-structure knows what to do. In addition, this approach leaves in hooks for doing more later.
It is not necessarily easy to nd compelling examples that give advantages for all steps. Adding in CiTO attributes to citations, for instance, has obvious advantages for the reader, but not the author. However, advantages may be indirect; richer reader semantics may give more readers and thus more citations| the thing authors appreciate as much as the act of publishing itself. It is, however, di cult to imagine how such advantages can be conveyed to the author at the point of writing. It is easy to see the advantages of semantic publishing for readers, as a community we need to pay attention to advantages to the authors. Without these \carrots", we will only have \sticks" and authors, particularly technically skilled ones, are highly adept at working around sticks.