Posts Tagged ‘beyondthePDF’

Supporting Reading

January 21st, 2011

Yesterday I spoke at Beyond the PDF about use cases for reading. Slides are below; the presentation was also webcast, so I hope to share a video recording when it becomes available. The video is now on Youtube (part of the Beyond the PDF video playlist) and below.

Thanks to the DERI Social Software Unit for feedback on an earlier version of this presentation. I’m particularly grateful to Allen Renear and Carole Palmer from UIUC, whose call for ontology-aware reading tools pushed me down this path, and to Geoffrey Bilder who presented these ideas in a way I couldn’t help thinking about and remixing. Cathy Marshall’s clear exposition, in Reading and Writing the Electronic Book was fundamental to digging deeper.

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Posted in books and reading, future of publishing, library and information science, scholarly communication, social semantic web | Comments (2)

6 quotes from Beyond the PDF – Annotations sessions

January 19th, 2011

Moderator Ed Hovy picked out 6 quotes to summarize Beyond the PDF’s sessions on Annotation.

Papers are stories that persuade with data.

But as authors we are lazy and undisciplined.

Communicating between humans and humans and humans and machines.

I should be interested in ontologies, but I just can’t work up the enthusiasm.

Christmas tree of hyperlinks.

You will get sued.

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Wanted: the ultimate mobile app for scholarly ereading

January 7th, 2011

Nicole Henning suggests that academic libraries and scholarly presses work together to create the ultimate mobile app for scholarly ereading. I think about the requirements a bit differently, in terms of the functional requirements.

The main functions are obtaining materials, reading them, organizing them, keeping them, and sharing them.

For obtaining materials, the key new requirement is to simplify authentication: handle campus authentication systems and personal subscriptions. Multiple credentialed identities should be supported. A secondary consideration is that RSS feeds (e.g. for journal tables of contents) should be supported.

For reading materials, the key requirement is to support multiple formats in the same application. I don’t know of a web app or mobile app that supports PDF, EPUB, and HTML. Reading interfaces matter: look to Stanza and Ibis Reader for best-in-class examples.

For organizing materials, the key is synergy between the user’s data and existing data. Allow tags, folders, and multiple collections. But also leverage existing publisher and library metadata. Keep it flexible, allowing the user to modify metadata for personal use (e.g. for consistency or personal terminology) and to optionally submit corrections.

For keeping materials, import, export, and sync content from the user’s chosen cloud-based storage and WebDAV servers. No other device (e.g. laptop or desktop) should be needed.

For sharing materials, support lightweight micropublishing on social networks and email; networks should be extensible and user-customizable. Sync to or integrate with citation managers and social cataloging/reading list management systems.

Regardless of the ultimate system, I’d stress that device independence is important, meaning that an HTML5 website would probably the place to start: look to Ibis Reader as a model.

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Searching for LaTeX code (Springer only)

January 6th, 2011

Springer’s LaTeX search service (example results) allow searching for LaTeX strings or finding the LaTeX equations in an article. Since LaTeX is used to markup equations in many scientific publications this could be an interesting way to find related work or view an equation-centric summary of a paper.

You can provide a LaTeX string, and Springer says that besides exact matches they can return similar LaTeX strings:
exact matches to a LaTeX search

Or, you can search by DOI or title to get all the equations in a given publication:
results for a particular title

Under each equation in the search results you can click “show LaTeX code”:
show the LaTeX code for an equation
Right now it just searches Springer’s publications; Springer would like to add open access databases and preprint servers. Coverage even in Springer journals seems spotty: I couldn’t find two particular discrete math articles papers, so I’ve written Springer for clarification. As far as I can tell, there’s no way to get from SpringerLink to this LaTeX search yet: it’s a shame, because “show all equations in this article” would be useful, even with the proviso that only LaTeX equations were shown.

A nice touch is their sandbox where you can test LaTeX code, with a LaTeX dictionary conveniently below.

via Eric Hellman

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Posted in future of publishing, information ecosystem, library and information science, math, scholarly communication | Comments (1)

The Social Semantic Web – a message for scholarly publishers

November 15th, 2010

I always appreciate how Geoffrey Bilder can manage to talk about the Social Semantic Web and the early modern print in (nearly) the same breath. See for yourself in the presentation he gave to scholarly publishers at the International Society of Managing and Technical Editors last month.

Geoff’s presentation is outlined, to a large extent, in an interview Geoff gave 18 months ago (search “key messages” to find the good bits). I hope to blog further about these, because Geoff has so many good things to say, which deserve unpacking!

I especially love the timeline from slide 159, which shows that we’re just past the incunabula age of the Internet:

The Early Modern Internet

We're still in the Early Modern era of the Internet. Compare to the history of print.

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Posted in future of publishing, information ecosystem, PhD diary, scholarly communication, semantic web, social semantic web, social web | Comments (3)

Accessing genomics workflows from Word documents with GenePattern

November 14th, 2010

What if you could rerun computational experiments from within a scientific paper?

The GenePattern add-on for Word for Windows integrates reusable genomic experiment pipelines into Microsoft Word. Readers can rerun the original or modified experiments from within the document by connecting to a GenePattern server.

Rerunning a pipeline inside Word

Rerunning a pipeline inside Word

I don’t run Windows, so I took this screenshot from a video produced at the Broad Institute of MIT and Harvard, where GenePattern is developed.

Readers without Word for Windows can also access the experimental pipelines by exporting them from the document: just run a GenePatternDocumentExtractor command from a GenePattern server. The GenePattern public server was very easy to access and start using. Here’s what the GenePatternDocumentExtractor command looks like:

Running GenePatternDocumentExtractor at the GenePattern public server

Running GenePatternDocumentExtractor at the GenePattern public server

Unfortunately the jobs I ran didn’t extract any pipelines from the Institute’s sample DOC. I’ve sent in an inquiry (either I’m doing something wrong or there’s a bug, either way it’s useful). I was very impressed that I could make my jobs public, then refer to them by URL in my email, to make clear what exactly I did.

The GenePattern add-on for Word is another find from the beyondthepdf list. Its development was funded by Microsoft. See also Accessible Reproducible Research by Jill P. Mesirov (Science, 327:415, 2010). doi:10.1126/science.1179653, which describes the underlying philosophy: have a Reproducible Research System (RRS) made up of an environment for doing computational work (the Reproducible Research Environment or RRE) and an authoring environment (the Reproducible Research Publisher or RRP) which links back to the research system.

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Utopia Documents: pulling scientific data into the PDF for interactive exploration

November 14th, 2010

What if data were accessible within the document itself?

Utopia Documents is a free PDF viewer which recognizes certain enhanced figures, and fetches the underlying data. This allows readers to view and experiment with the tables, graphs, molecular structures, and sequences in situ.

You can download Utopia Documents for Mac and Windows to view enhanced papers, such as those published in The Semantic Biochemical Journal.

These screencasts were made from pages 9 and 10 of PDF of a paper by the Manchester-based Utopia team: T. K. Attwood, D. B. Kell, P. Mcdermott, J. Marsh, S. R. Pettifer, and D. Thorne. Calling international rescue: knowledge lost in literature and data landslide! Biochemical Journal, Dec 2009. doi:10.1042/BJ20091474.

In an interview at the Guardian, Utopia’s Phillip McDermott says:

“Utopia Documents links scientific research papers to the data and to the community. It enables publishers to enhance their publications with additional material, interactive graphs and models. It allow the reader to access a wealth of data resources directly from the paper they are viewing, makes private notes and start public conversations. It does all this on normal PDFs, and never alters the original file. We are targeting the PDF, since they still have around 80% readership over online viewing.

“Semantics, loose-coupling, fingerprinting and linked-data are the key ingredients. All the data is described using ontologies, and a plug-in system allows third parties to integrate their database or tool within a few lines of script. We use fingerprinting to allow us to recognise what paper a user is reading, and to spot duplicates. All annotations are held remotely, so that wherever you view a paper, the result is the same.”

I’d still like to see a demo of the commenting functionality.

I’d also be particularly interested in the publisher perspective, about the production work that goes into creating the enhancements. Portland Press’s October news announces that they’ve been promoting Utopia at the Charleston conference and SSP, with an upcoming appearance at the STM Innovations Seminar.

Utopia came to my attention via Steve Pettifer’s mention.

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Posted in future of publishing, information ecosystem, library and information science, scholarly communication, semantic web, social semantic web | Comments (4)

A Model-View-Controller perspective of scholarly articles

November 13th, 2010

A scholarly paper is not a PDF. A PDF is merely one view of a scholarly paper. To push ‘beyond the PDF’, we need design patterns that allow us to segregate the user interface of the paper (whether it is displayed as an aggregation of triples, a list of assertions, a PDF, an ePub, HTML, …) from the thing itself.

Towards this end, Steve Pettifer has a Model-View-Controller perspective on scholarly articles, which he shared in a post on the Beyond the PDF listserv, where discussions are leading up to a workshop in January. I am awe-struck: I wish I’d thought of this way of separating the structure and explaining it.

I think a lot of the disagreement about the role of the PDF can be put down to trying to overload its function: to try to imbue it with the qualities of both ‘model’ and ‘view’. … One of the things that software architects (and I suspect designers in general) have learned over the years is that if you try to give something functions that it shouldn’t have, you end up with a mess; if you can separate out the concerns, you get a much more elegant and robust solution.

My personal take on this is that we should keep these things very separate, and that if we do this, then many of the problems we’ve been discussing become more clearly defined (and I hope, many of the apparent contradictions, resolved).

So… a PDF (or come to that, an e-book version or a html page) is merely a *view* of an article. The article itself (the ‘model’) is a completely different (and perhaps more abstract) thing. Views can be tailored for a particular purpose, whether that’s for machine processing, human reading, human browsing, etc etc.

[paragraph break inserted]

The relationship between the views and their underlying model is managed by the concept of a ‘controller’. For example, if we represent an article’s model in XML or RDF (its text, illustrations, association nanopublications, annotations and whatever else we like), then that model can be transformed in to any number of views. In the case of converting XML into human-readable XHTML, there are many stable and mature technologies (XSLT etc). In the case of doing the same with PDF, the traditional controller is something that generates PDFs.

[paragraph break inserted]

The thing that’s been (somewhat) lacking so far is the two-way communication between view and model (via controller) that’s necessary to prevent the views from ossifying and becoming out of date (i.e. there’s no easy way to see that comments have been added to the HTML version of an article’s view if you happen to be reading the PDF version, so the view here can rapidly diverge from its underlying model).

[paragraph break inserted, link added]

Our Utopia software is an attempt to provide this two-way controller for PDFs. I believe that once you have this bidirectional relationship between view and model, then the actual detailed affordances of the individual views (i.e. what can a PDF do well / badly, what can HTML do well / badly) become less important. They are all merely means to channeling the content of an article to its destination (whether that’s human or machine).

The good thing about having this ‘model view controller’ take on the problem is that only the model needs to be pinned down completely …

Perhaps separating out our concerns in this way — that is, treating the PDF as one possible representation of an article — might help focus our criticisms of the current state of affairs? I fear at the moment we are conflating the issues to some degree.

– Steve Pettifer in a Beyond the PDF listserv post

I’m particularly interested in hearing if this perspective, using the MVC model, makes sense to others.

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