I have a PhD studentship available for anyone wishing to work on using the Semantic Web and linked data to improve the process of scientific publishing.

I want to expand on the work that we have done with Kcite (http://www.russet.org.uk/blog/2012/02/kcite-spreads-its-wings/), which links between different articles, and consider how we would link to and from both raw data and ontological resources. We will do this in a practical, real-world environment: we will be extending WordPress server-side; all the tools that we generate we will be released as we go into the “wild”; we will be active at supporting users so that we can incorporate feedback. We will be targetting the academic blogosphere, in addition to working with the content on http://knowledgeblog.org.

If you are interested, please feel free to email me directly. The full details of the advert are below.

Advert

http://www.ncl.ac.uk/postgraduate/funding/search/list/cs024

The linked data initiative seeks to increase the machine computability of the web, but it is hard for authors to generate linked-data. We will investigate ways of publishing scientific knowledge where authors, readers and computational agents all gain advantage from additional semantics and machine computability. We will investigate representation of graph data and deep linking to ontological resources.

This project will feed into Knowledgeblog (http://knowledgeblog.org) which is both a high traffic (100k+ page reads) academic site in its own right, as well releasing its software for third party use by the academic blogosphere. Combined with exemplars using real data where possible, this will provide two valuable routes to evaluate and assess the representations in a real-world environment.

Value of the Award of Eligibility

Depending on how you meet the EPSRC criteria (http://www.epsrc.ac.uk/funding/students/pages/eligibility.aspx.) you may be entitled to a full or partial award. A full award covers tuition fees at the UK/EU rate and an annual stipend of £14,790 (2012/13). A partial award covers fees at the UK/EU rate only. The studentship is not available for candidates from outside of the EU.

Person Specification

You should have either a First class honours degree in Computing Science, Mathematics, or other relevant science or engineering subject, or a or 2.1 in Computing Science, Mathematics or other relevant science or engineering subject and a distinction level Masters degree in a related subject. Equivalent experience will also be considered.

How to Apply

Apply through the University’s online postgraduate application form insert the reference CS024 and select ‘PhD COMP’, with programme code 8050F, as programme of study. Mandatory fields need to be completed and a covering letter, CV and (if English is not your first language) a copy of your English language qualifications attached. The letter must state the title of studentship, quote reference CS024 and describe how your research interests fit with the topic of the research projected outlined (max. 2 pages). If you already have published research papers a list of these providing bibliographic details should be included in the letter.

You should also send your covering letter and CV to the Postgraduate Secretary at cs.pg@ncl.ac.uk.

Further Information

For further details, please contact Phillip Lord (phillip.lord@newcastle.ac.uk), 0191 222 7827

Bibliography

1 Introduction

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 (http://dx.doi.org/10.1109/MIS.2006.62)(http://dx.doi.org/10.1087/2009202)(http://dx.doi.org/10.1371/journal.pcbi.1000361). The idea of semantic publishing is an attractive one for those who wish to consume papers electronically; it should enhance the richness of the computational component of papers (http://dx.doi.org/10.1087/2009202). It promises a realisation of the vision of a next generation of the web, with papers becoming a critical part of a linked data environment (http://dx.doi.org/10.1109/MIS.2006.62),(http://dx.doi.org/10.4018/jswis.2009081901), where the results and naratives become one.

The reality, however, is somewhat different. There are significant 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 scientific publishing; while most journals have a website, the publication process still revolves around the generation of papers, moving from Microsoft Word or L^aT_eX (http://www.latex-project.org), through to a final PDF which looks, feels and is something designed to be printed onto paper (this includes conferences dedicated to the web and the use of web technologies). Adding semantics into this environment is difficult or impossible; the content of the PDF has to be exposed and semantic content retro-fitted or, in all likelihood, a complex process of author and publisher interaction has to be devised and followed. If semantic data publishing and semantic publishing of academic narratives are to work together, then academic publishing needs to change.

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—different kinds of knowledge that we wish to enhance. In the process, we add a small amount of semantics to the finished 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 significant limitations on the level of semantics that can be achieved, we believe that it does increase the likelihood that content will be generated in the first place, and represents an attempt to enable semantic publishing in a real-world workflow.

2 Knowledgeblog

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, finally, through to the knowledge domain (http://www.russet.org.uk/blog/2011/06/ontogenesis-knowledgeblog-lightweight-semantic-publishing/). However, we have found the traditional book publishing process frustrating and unrewarding. While scientific authoring is difficult in its own right, our own experience suggests that the publishing process is extremely hard-work. This is particularly so for multi-author collected works which are often harder for the editor than writing a book “solo”. Finally, the expense and hard copy nature of academic books means that, again in our experience, few people read them.

This contrasts starkly with the web-first 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 (http://www.wordpress.org), running on low-end hardware, and used it to develop a multi-author resource describing the use of ontologies in the life sciences (our main field of expertise). There are also kblogs on bioinformatics (http://bioinformatics.knowledgeblog.org) and the Taverna workflow environment (http://taverna.knowledgeblog.org)(http://dx.doi.org/10.1093/nar/gkl320). We have previously described how we addressed some of the social aspects, including attribution, reviewing and immutablity of articles (http://www.russet.org.uk/blog/2011/06/ontogenesis-knowledgeblog-lightweight-semantic-publishing/)

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 final paper, while living within the key constraint of making life (slightly) better for machine, author and reader without adding complexity for the human participants.

Scientific authors are relatively conservative. Most of them have well-established toolsets and workflows 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 ‘scientific’ articles are manifold. Many wish to be able to author while offline (particularly on trains or planes). Almost all scientific 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 L^aT_eX, because its idiomatic approach to programming documents is unreplicable with anything else. Fortunately, it is possible to induce WordPress to accept content from many different authoring tools, including Word and L^aT_eX (http://www.russet.org.uk/blog/2011/06/ontogenesis-knowledgeblog-lightweight-semantic-publishing/)

As a result, during the kblog project, we have seem many different workflows in use, often highly idiosyncratic in nature. These include:

Word/Email:

Many authors write using MS Word and collaborate by emailing files around. This method has a low barrier to entry, but requires significant social processes to prevent conflicting versions, particularly as the number of authors increases.

Word/Dropbox:

For the taverna kblog (http://taverna.knowledgeblog.org), authors wrote in Word and collaborated with Dropbox (http://www.dropbox.com). This method works reasonably well where many authors are involved; Dropbox detects conflicts, although it cannot prevent or merge them.

Asciidoc/Dropbox:

Used by the authors of this paper. Asciidoc (http://www.methods.co.nz/asciidoc) is relatively simple, somewhat programmable and accessible. Unlike L^aT_eX which can be induced to produce HTML with effort, 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-first”. 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 offer 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 specific to biology. In each case, we have taken a slightly different approach, but have fulfilled our primary aim of making life better for machine, author and reader.

3 Representing Mathematics

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 specific challenges because of its complexity, the difficulty of authoring and the difficulty of rendering, away from the chalk board that is its natural home.

Support for mathematics has had a significant impact on academic publishing. It was, for example, the original motivation behind the development of T_eX (http://en.wikipedia.org/wiki/TeX), and it still one of the main reasons why authors wish to use it or its derivatives. This is to such an extent that much mathematics rendering on the web is driven by a T_eX engine somewhere in the process. So MediaWiki (and therefore Wikipedia), Drupal and, of course, WordPress follow this route. The latter provides plugin support for T_eX markup using the wp-latex plugin (http://wordpress.org/extend/plugins/wp-latex/). Within kblog, we have developed a new plugin called mathjax-latex (http://wordpress.org/extend/plugins/mathjax-latex/) From the kblogauthor’s perspective these two offer a similar interface – differences are, therefore, described later.

Authors write their mathematics directly as T_eX using one of the four markup syntaxes. The most explicit (and therefore least likely to happen accidentally) is through the use of “shortcodes” (http://codex.wordpress.org/Shortcode).

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 “\(e=mc^2\)”. It is also possible to use three other syntaxes which are closer to math-mode in T_eX: $‍$e=mc^2$‍$, $latex e=mc^2$, or \‍[e=mc^2\‍].

From the authorial perspective, we have added significant value, as it is possible to use a variety of syntaxes, which are independent of the authoring engine. For example, a T_eX-loving mathematician working with a Word-using biologist can still set their equations using T_eX syntax; although Word will not render these at authoring time but, in practice, this causes few problems for such authors, who are experienced at reading T_eX. Within an L^aT_eX workflow 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 long-winded. A second issue, however, is that it is hard to integrate with existing workflows; most of the publication workflows we have seen in use will on recognising an angle bracket turn it into the equivalent HTML entity. For some workflows (L^aT_eX, 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 workflow. Ironically, it is because MathML shares an XML based syntax with the final 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 T_eX-like syntaxes has considerable advantages.

For the reader, the use of mathjax-latex has significant advantages. The default mechanism within WordPress uses a math-mode like syntax $‍latex e=mc^2‍$. This is rendered using a T_eX engine into an image which is then incorporated and linked using normal HTML capabilities. This representation is opaque and non-semantic; it has significant 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 reflect the local style.

Kblog, however, uses the MathJax library (http://www.mathjax.org) this has a number of significant advantages for the reader. First, where the browser supports them, MathJax uses webfonts to render the images; these are scalable, attractive and standardized. Where they are not available, MathJax can fall-back to bitmapped fonts. The reader can also access additional functionality: clicking on an equation will raise a zoomed in popup; while the context menu allows access to a textual representation either as T_eX or MathML irrespective of the form that the author used. This can be cut-and-paste for further use. Kblog uses the MathJax library (http://www.mathjax.org) to render the underlying T_eX directly on the client.

Our use of MathJax provides no significant 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 T_eX 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 equations 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 T_eX style markup appears accidentally elsewhere in the document), the author is likely to have seen this and fixed 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 MathJax (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).

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 a bit. In short, we provide a practical mechanism to identify text containing mathematics and a mechanism to transform this to a single, standardised representation.

4 Representing References

Unlike mathematics, there is no standard mechanism for reference and in-text citation, but there are a large number of tools for authors such as BibTeX, Mendeley (http://www.mendeley.org) or EndNote. As a result of this, the integration with existing toolsets is of primary importance, while the representation of the in-text citations is not, as it should be handled by the tool layer anyway.

Within kblog, we have developed a plugin called kcite (http://wordpress.org/extend/plugins/kcite/). For the author, citations are inserted using the syntax:[‍cite]10.1371/journal.pone.0012258[‍/cite]. The identifier used here is a DOI, or digital object identifier and, is widely used within the publishing and library industry. Currently, kcite supports DOIs minted by either CrossRef (http://www.crossref.org) or DataCite (http://www.datacite.org) (in practice, this means that we support the majority of DOIs). We also support identifiers from PubMed (http://www.pubmed.org) which covers most biomedical publications and arXiv (http://www.arxiv.org), the physics (and other domains!) preprints archive, and we now have a system to support arbitrary URLs. Currently, authors are required to select the identifier where it is not a DOI.

We have picked this “shortcode” format for similar reasons as described for maths; it is relatively unambiguous, it is not XML based, so passes through the HTML generation layer of most authoring tools unchanged and is explicitly supported in WordPress, bypassing the need for regular expressions and later parsing. It would, however, be a little unwieldy from the perspective of the author. In practice, however, it is relatively easy to integrate this with many reference managers. For example, tools such as Zotero (http://www.zotero.org) and Mendeley use the Citation Style Language, and so can output kcite compliant citations with the following slightly elided code:

 <citation>
    <layout prefix="[‍cite]" suffix="[‍/cite]"
         delimiter="[‍/cite] [‍cite]">
      <text variable="DOI"/>
    </layout>
  </citation>

We do not yet support L^aT_eX/BibTeX citations, although we see no reason why a similar style file should not be supported (citations in this representation of the article were, rather painfully, converted by hand). We do, however, support BibTeX-formatted files: the first 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:

(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 identifiers to references. This simplifies 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 identifiers are checked; if they are wrong, the authors will see this straightforwardly as the entire reference will be wrong. Adding DOIs or other identifiers moves from becoming a burden for the author to becoming a specific advantage.

While supporting multiple forms of reference identifier (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 request per reference (in practice, it is often more; DOI requests, for instance use 303 redirects), 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 finally 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 finally in-text citations are linked both to the bibliography and directly through to the external source. Currently, the format of the reference list is fixed, however, citeproc-js is a generalised reference processor, driven using CSL (http://citationstyles.org/). 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 resources (where the identifier allows — PubMed IDs redirect to PubMed). 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.

For the computational agent wishing to consume bibliographic information, we have added significant 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 identifiers are, again, likely to be correct because the authors now need them to be correct for their own benefit.

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) interpretation of the primary data.

A final, and subtle, advantage of kcite is that the authors can only use public metadata, and not their own. If they use the correct primary identifier, and still get an incorrect reference, it follows that the public metadata must be incorrect (or, we acknowledge, that kcite is broken!). Authors and readers therefore must ask the metadata providers to fix their metadata to the benefit 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 (http://dx.doi.org/10.1093/nar/gkg091). Authors do this placing an ArrayExpress identifier which has the form E-MEXP-1551. Currently, adding this identifier to a publication, as with adding the raw data to the repository is no direct advantage to the author, other than fulfilment of the publication requirement. Similarly, there is no existing support within most authoring environments for adding this form of reference.

For the knowledgeblog-arrayexpress plugin (http://knowledgeblog.org/knowledgeblog-arrayexpress), therefore, we have again used a shortcode representation, but allowed the author to automatically fill 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 significant. 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 (see Section ), the use of an identifier becomes an advantage rather than a burden to the authors.

Currently, for the reader there is less significant advantage at the moment. While there is some value to the author of the added correctness stemming from the ArrayExpress identifier. However, knowledgeblog-arrayexpress is currently under-developed, and the added semantics that is now present could be used 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 (http://www.ncbi.nlm.nih.gov/Taxonomy/).

Likewise, advantage for the computational agent from knowledgeblog­-array­express is currently limited; the identifiers 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 knowledgeblog­-array­express, 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 specific species using standardised nomenclature (the standard nomenclature was only invented in 1753 and is still not used universally) would be a considerable boon.

5 Discussion

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 different aspects of authoring and publishing to be over-turned. More over, we have followed a strong principle of semantic enhancement which offers advantages to both reader and author immediately. So, adding references as a DOI, or other identifier, ‘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 first 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 significant compromise. We offer here two examples.

First, there has been significant work by others on CiTO (http://dx.doi.org/10.1186/2041-1480-1-S1-S6) – an ontology which helps to describe the relationship between the citations and a paper. Kcite lays the ground-work for an easy and straight-forward addition of CiTO tags surrounding each in-text citation. Doing so, would enable increased machine understandability of a reference list. Potentially, we could use this to the advantage to the reader also: we could distinguish between reviews and primary research papers; highlight the authors’ previous work; emphasise older papers which are being refuted. However, to do this requires additional semantics from the author. Although these CiTO semantic enhancements would be easy to insert directly using the shortcode syntax, most authors will want to use their existing reference manager which will not support this form of semantics; even if it does, the author themselves gain little advantage from adding these semantics. There are advantages for the reader, but in this case not for both author and reader. As a result, we will probably add such support to kcite; but, if we are honest, find it unlikely that when acting as content authors, we will find the time to add this additional semantics.

Second, our presentation of mathematics could be modified to automatically generate MathML from any included T_eX 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 offers the possibility of the most specific and increased level of semantics of all of our plugins. Knowledge about a species or a microarray experimental design can be precisely represented. However, almost by definition, 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 offer 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 scientific publishing adds up to one large one.

6 Conclusion

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 benefit to readers, authors and computational interpretation. As a result, at this stage, we have light semantic publishing, but with small, but definite benefits for all.

Semantics give meaning to entities. In kblog, we have sought benefit by “saying” within the kblog environment that entity x is either maths, a citation or a microarray data entity reference. This is sufficient for the kbloginfra-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 benefit from it looking like maths; the author has benefit 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 find 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, difficult 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.

Bibliography

Today, I was pleased to release version 1.5 of kcite. Follwing in my tradition of being unable to get the WordPress plugin release process to work correctly, shortly after I released 1.5.1 which is the same thing, but with the correct metadata.

I’m quite pleased with this release. There have been some underlying changes to the technology which I will describe in another post, but for now I want to focus on what I feel represents a substantial improvement on previous versions in terms of functionality. The previous release added support for client-side rendering, which made things look nicer and will add more functionality into the future. However, from an authoring perspective this did not provide much advantage.

For the 1.5 release, I wanted to add new forms of identifier. Kcite started with the ability to cite digitial object identifiers to papers, as this reference to one of my papers shows (http://dx.doi.org/10.1371/journal.pone.0012258). As a bioinformatician, references to PubMed also seemed like a good idea (http://www.ncbi.nlm.nih.gov/pubmed/21414991), even if, in most cases a doi could be used also.

However, for this release, I wanted to expand into two new areas. Kcite has come from the kblog project where we have been trying to improve the formality of publication using a blog engine, so that it can become an recognised part of the scientific literature. Organisations like arxiv have done much the same thing (with far greater success!) with preprint. It makes sense then that kcite can now also link straight through to here also (http://arxiv.org/abs/1109.4518). Likewise, we wanted to support the push to data citation, which we have achieved courtesy of datacite. It is now possible to reference data sets also (http://dx.doi.org/10.5524/100005).

And, finally, I have tidied up the presentation. Every item now has a visible URI in the reference list. I have made it visible because these identifiers should be public and present, not just providing an underlying link structure, although they do this as well now. In text citations link through to the bibliography, but also provide an outlink, direct to the resource also. Before processing, the underlying text citation displays the URI which should aid machine interpretability. This link will also be correct, since it is used to gather the metadata for the citation, rather expecting authors to tack a URI to a citation that already appears correct to them.

As always, new forms of publication raise questions and this release is no exception. We have, for instance, found that kblogs are useful for publishing grey literature such as bio-ontologies. But at the moment, rather embarrasingly, there is no way to reference these articles (or indeed this article itself!) with KCite. And, second, there is an issue of provenance. For instance, the notice describing the 1.4 release of kcite is now formatted with 1.5. It’s changed since it’s original publication because I have upgraded Kcite, as in turn will the presentation on this article change with the next release. I am hoping to address both of these issues in the near future.

Bibliography

While I am currently spending a significant amount of my time promoting the idea that blog technology can be, and should be used for serious scientific material, I thought I would make a post of a different and perhaps more traditional vein: that is, a light-weight idea, with no serious research behind it, but Years ago now, I created an Energy Wiki full of daft ideas for making energy. I last revisted this in 2009, with an idea for storing energy at sea. I’d actually forgotten that part of the reason for this was to try out Inkscape, which is part of the reason for this post. I wanted to try a bit of multi-media, that is, a blog post with an image in it. High tech.

So, the idea. One form of renewable is the Solar Updraft Tower, also known as a solar chimney. This works straightforwardly enough: you build a large greenhouse in a desert, with a very large chimney in the middle. The top of the chimney is in cold air, the bottom in hot, and an updraft results; stick a turbine in or at the base of the chimney, and you get energy out.

The problem is to work at all efficiently, you need a big temperature differential, so a tall chimney. This in turn means a wide chimney, both to support a substantial updraft, and for mechanical reasons. Tall means 500m or more. The bottom line of this is that a pretty significant capital expenditure is required, followed by a relatively long pay-back period, which in turn means that the biggest single expense of the project is likely to be interest charges, rather than anything else.

So, my idea, is to use an inflatable chimney instead. Initially, I thought about some kind of helium lifting scheme, but then I realised that this makes no sense; why not use hot air, which after all is what the whole system is designed to generate. Consider, for instance, the following organisation:

Essentially, it’s a traditional balloon with a hole in the middle. Obviously the whole system is stackable — a second balloon could be placed on top of the first and so on. The whole structure could be assembled or dissassembled as desired. Unfortunately, though this would probably take quite a bit of work.

My second thought came from the idea that, while most designs for solar chimneys have the chimney in the middle of the greenhouse, it doesn’t really need to be. A horizontal pipe to the middle would be enough. The chimney could be outside of the greenhouse. The advantage that this brings is that the tower could be raised or lowered in-situ, without the risk of it falling on, and damaging the greenhouse. So my second idea was to build the chimney as a two cylinders, with the gap between the serving as the inflatable, buoyant structure. By pleating the cylinders in opposite directions like so:

the whole structure should concertina up and down. By inflating from the top and deflating from the bottom, it should be possible to raise or lower the entire system by opening and shutting vents at the bottom or top of each section to the inside of the chimney.

One advantage with this system, is that as the chimney gets higher, the temperature differential between the inside and the outside gets greater, which should mean that the taller the tower, the more bouyant the sections get; this should help to keep the entire thing as upright as possible, as will the air travelling through the middle, like some gigantic party blower.

Another addition that cames to mind would be to add inflatable half-toroids around the chimney at regular intervals. With a curve on the top, and a flat bottom-side, the entire thing should operate like an aerofoil, lifting the tower up; so, the windier it gets, the greater the lift, which is just what is needed to keep it as upright as possible. This should mean that the chimney can operate in relatively high wind levels.

This kind of system could even work in concert with a fixed chimney — extending the height by 500m say, and increasing it’s efficiency. It could also act as a supplement — operating only on very hot days when the greenhouse has excess capacity. Or, finally, it could operate while the main chimney was being built, meaning that a plant can start generating income earlier, which should reduce the cost of interest payments.

Of course, this all comes with drawbacks: the ongoing running costs are likely to be a significant; wind will remain a significant factor regardless; and, finally, inflating the tower will using hot air, which will reduce the efficiency of the whole system. Are these flaws significant? Well, as I said, this post is light-weight with no serious research behind it. I have no idea, nor any really clear idea about how to work out these costs. Answers on a postcard please.

I have been pushing the idea of Kblogs — scientific publishing using commodity software — for a year or so know. Our main site, Knowledgeblog.org has got around 100 articles now, and has had about 50k page views (or about 4x the number of raw page hits) and has generated a certain presence on the internet. While this is generally good, the price of fame is that we have moved somewhat up the list of potential hack targets. Unfortunately, this has resulted in two compromises on the machine; they were probably not disconnected, although we have no evidence to link the two at the moment.

The first was through the timthumb zero day vulnerability. It involved a code injection into a WordPress installation using a thumb nail generator with a dodgy bit of PhP in it. We cleaned the system up as well as we are able and went from there. Sadly, a couple of days ago, we had a second break in. This was a more serious and directed attack (the timthumb was scripted, and we were one of several thousands of sites to be hit). In this case, the machine has been root compromised, and the web server used to gather username/passwords in a phishing expedition. We do have backups and all of the content. There were a number of things that we could have done to secure the machine further, at least one of which may have prevented the hack, but there are only so many hours in the day.

So, where does this leave us? Is the whole idea of knowledgeblog broken? Personally, I do not think so. While I have been critical of the cost associated with academic publishing, I am aware that it cannot happen for free. Running and maintaining a web server takes money; it is something that we have been doing on a shoe-string for a while, especially since our JISC money ran out. In the couple of years that we have run knowledgeblog, I think that we have learned and shown a lot. As well as page views and content, we have shown that scientific publishing can be easy for the author; that we can generate attractive articles this way; that we can start to embed computational accessible knowledge into these articles. We have shown that we can do peer-review, if we need. We have shown we can archive and preserve for the future. We have shown that knowledgeblog is good for grey literature. We have added DOIs. Multiple authors. Good looking maths. We even have some preliminary stats on how much publication costs from Word doc to website.

At the moment, though, we do not have a business model. It is clear that if we are to move this forward, it needs to be run as a service, managed, and looked after, something which is neither my expertise or desire. The analogy that I have made earlier with Wikipedia is, I think, a good one; it would be good to move this into a foundation status.

The path from here to there is a long one, however. For the moment, we will restore knowledgeblog, and it will re-emerge, although at this time of year, it will take a while. But we look to the future as well.

Although in some disciplines, it is relatively uncontentious, the rise of open access publishing has produced a lot of comment in others. In one of my two disciplines, computing science, this form of publication is still the minority, and still raises comment. For instance, Michel Beaudouin-Lafon has commented suggesting this scientists are highly naive about the costs of publishing. He argues that scientific publishing is intrinsically expensive, and that open access will have negative implication for science as a whole.

Over the years, commercial STM publishing has become a cutthroat business with cutthroat practices and we, the scientific and academic community, are the naive lambs, blinded by the ideals of science for the public good-or simply in need of more publications to advance our careers.

— Michel Beaudouin-Lafon

Personally, I think that “naive” is the wrong word; scientists are often not good at operating in a co-ordinated way. Although, we work together in small groups, and sometimes in large groups, in general, we are still very much a cottage industry; at any one time the number of scientists working in a distinct discipline is not that large, even on a world-wide basis. Of course, this works pretty well for scientific advance; we are not a production industry, but researcher. No one knows the best way forward, and we need to experiment to find out. But it does mean that we often play second fiddle to those capable of more co-ordinated action; compare for example, scientists to the medical community with its tightly controlled professional bodies. Or, of course, the STM publishing industry, particularly as it has become focused in fewer and fewer competing publishers.

For example, ACM spends several million dollars every year to support the reliable data center serving the Digital Library

— Michel Beaudouin-Lafon

Clearly, it is true that the cost of data centres and storage are not trivial. But the cost of servicing data has plummeted over recent years. Scientific papers largely consist of storing words and figures; these do not take up much space. The laptop I am working on has a copy of my email directory; it’s not complete but it carries most of my outgoing email since 1994 and a lot of the incoming; this is a lot of words! But the total size is now less than 5G, which will fit on a 3 pound pen drive, or my phone. Now if ACM were storing research data, then it would be a totally different issue; the costs here are significant, problematic and rising. But they do not.

The ACM might spend several million dollars a year, but the bottom line here is that this does not account for the cost of publishing. The Wikimedia foundation which supports Wikipedia spends around 10 million dollars a year, in total, on one of the top ten websites in the World. This is about the daily cost of the whole scientific publishing industry.

The quality of a journal is typically measured by its impact factor

— Michel Beaudouin-Lafon

And a very bad measurement of journal quality it is too. As someone who works in two disciplines at once, I constantly get hit by this: my best computing publications have laughable impact factors when compared to my bio publications; when judged against computer scientists, however, my bio publications have such high impact factors, that they have to be ignored as outliers.

At $5,000 per publication, my lab is broke.

— Michel Beaudouin-Lafon

It is not clear where the $5,000 figure comes from, as most open access is less than this. But, anyway, this argument makes no sense. Our labs are already paying a vast amount of money for publications; usually this is squirrelled away in overheads, taken from our budgets before we see the money. And, although it doesn’t happen so much in computing, many journals levy significant page charges.

They are the big pharmaceutical labs and the tech firms who publish very little but rely on the publication of scientific results for their businesses. With author-pay, research will pay so that industry can get their results for free. Is this moral?

— Michel Beaudouin-Lafon

Open access on its own is not enough. we also need public disclosure about the process. Perhaps the examples of the pharmaceutical funding journals directly are unusual. It is not so easy to tell at the moment. In this context, it could be argued that the last thing we need is the pharmaceutical industry paying for the results of science. Of course, conversely, the pharmaceutical industry could argue that they already do pay for the (publically funded) research by way of taxation.

While they are interesting, all of these arguments really miss the point: the pharmaceutical industry already get their results for free, as their subscription fees do NOT pay for the research just its publication. The publishing industry also get the results that they depend on for free or with page-charges by charging the authors. And for every paper that researchers publish for free, they pay more to read someone elses.

So, we are already in the situation that we are told is not moral.

It is important to understand that the scientific community is largely at fault

— Michel Beaudouin-Lafon

There is some truth in the idea that scientific community has let itself walk into the situation, but ultimately I feel, that this is like blaming the financial crises on those recieving subprime mortgages. It is true that it is scientists who submit their best work to expensive closed publishers; but, especially in early and mid “career”, we do this to safe-guard our futures.

The problem with the subscription model is not the model but the fees.

— Michel Beaudouin-Lafon

Quite the opposite. Ultimately, I don’t pay the fees, so how much do I really care? But the subscription model prevents re-purposing, it limits access, it prevents competition. I work at a university as a scientist because I value the ability to be able to swap and discuss my work. I want the general public to be able to access my research. Dissemination of knowledge should be part of my job; I think it is reasonable that I, or my employers, should pay for it.

Which is not to say that the level of fees are fine; they are not. They are far to expensive under any model.

The added value provided by publishers is twofold: reputation (the value of the imprimatur), and archiving (the guarantee that the work will be available forever).

— Michel Beaudouin-Lafon

And this is it? Is this all that we are getting, given the costs? Especially the the reputation comes from the work, not the journal, and the archiving should be a rapidly decreasing cost.

Actually, in practice, I think the current publishing industry brings more value; selection of reviewers, sometimes copy-editing and, critically, advertising of the content. But, again, times have changed, and publishing practice in these areas has not.

The only other area in publishing where authors pay to get published is called the vanity press. Do we really want to enter that model?

— Michel Beaudouin-Lafon

This is a low blow, nor is it true. Many people pay for their own publishing costs. The government pays to publish election results; health service pay to publish public health information; companies pay to publish product safety recalls. All circumstances where the value to the author of public awareness of their content far exceeds the income they would recieve from charging. And the biggest example of this is the advertising industry.

Nor is the implication that this will necessarily result in low quality true. Consider the blogosphere; of course, there is much junk, the standard of science journalism is very high; frankly, when ever respecting sources like the BBC start talking about pixie dust, it’s probably at least as high-standard the as mainstream media.

All this aside, what do I, as a scientist, actually care about? Some of these leap to mind:

• Stable location and content.
• archiving
• peer review
• discovery and selection

Open access was built on the basis of replicating the existing publication. PLoS for example did this precisely so that it did not challenge both the business model and the publication procedure at the same time. How much of the costs stem from this? I think that we, as authors and readers, should know. How much of the millions the ACM spends on it’s data centre is involved in managing access controls, for example? How much on advertising? How much at booths at meetings?

Open access has opened the door, but now we need to challenge and change the process. Hosting data is not free nor is archiving. And, yet, I can find own my website from 2002 and enjoy it’s gaudy colour scheme all again. If this blog post is so exciting to the world, that the load brings the server down, you will be able to read it on coral cache. The peer review is expensive and time-consuming; I know because I’ve organised enough of it for BioOntologies. But then I did not get paid for this and how many of the real costs of peer-review do publishers bear? And discovery and selection? Well, we have google, and I follow my peers on twitter.

Author fees are not a solution. […] Finally, nonprofit publishers should take advantage of their unique position to experiment with sustainable evolutions of their publishing models.

— Michel Beaudouin-Lafon

And on this, I could not agree more. Our experiment with Knowledgeblog suggests that we can get 90% (or 80% or 70% depending on who you ask) with commodity software. It’s only a small start, but then I was on the mailing list that saw the first email about the creation of wikipedia, and that wasn’t long ago.