This one shows the whole hierarchy but you cant read any node from the graph (it’s in zoom out). Producing attractive publications
First screenshot showing an article and some metadata on the right side. The metadata showed in the following sequence: A chemical structure of a small molecule taken from ChemBl. Then follows the explanation of this molecule taken from wikipedia and finaly some references on related papers taken from pubmed Producing attractive publications
The metadata on this article are taken from wikipedia and shows info about the Shikinate kinase enzyme. Producing attractive publications
This is a screenshot of a paper from Phil Bourne on the Mycobacterium tuberculosis 'drugome', to which UD has added information from (in order) 1) PLoS (showing article level metrics for this article) 2) Crossref (giving a cut-and-pasteable citation for this document, which you can change to fit your journal style) 3) AltMetric, showing its altmetric score and where this article has been mentioned on the web 4) Sherpa/Romeo, showing the archiving policy for this article 5) Mendeley, showing other related articles 6) A hyperlinked version of the article's bibliography Producing attractive publications
Consider for example this process from one of the major publishers that I have Published with. I wrote my article in latex. I converted it to PDF. The website converted it to another PDF (which I had to check). The publishers then (and this is true) converted it to a word doc. From there, they turn it into XML, which was finally converted to HTML and, yes, you guessed It, another PDF. Now, not only is this a waste of time, but it’s inaccurate. Errors happen. And trying to get Structured or data linked publications through this process. You might as well give up.
What does it all mean anyway
What does it all mean anyway?
University of Manchester, UK
So, what am I going to do?
• Define some terms
• Pose lots of questions
• Introduce some concepts
• Set some Challenges
• Solve semantic publication
First catch your terms
• Publication: Exposure to the public (sic) OF SOME
• Publication – the process (the act) and the published
• Semantic: capturing the meaning of information in
some computationally amenable form
• Authoring: The process of “WRITING” some WORK
• Semantic Web: The Web plus computational
• Things on the Web are published
• A publication enhanced with semantics
• We usually think of a publication as an article – some
• But what about ontologies and semantic data?
• Are these not semantic publications too?
• An ontology should capture knowledge of a field of interest in
a computationally amenable form and it is published on the
• RDF descriptions of some data, enhanced with some defined
vocabulary, are a semantic publication of those data
• bio2RDF and all its constituent parts
• “Published to the linked data cloud”
Post processing of articles with text
mining and NLP
• Marking up entities with text mining
• Named entity recognisers for different types of
• Normalised to identifiers – could add
semantics and other TM to give relationships
• AO and all that
Embedding semantics into scholarly
articles• But I could do all of this from the
start if my tools were good
• Methods and data might be the
easiest to make semantic from
• Even “easier” would be
rhetorical blocks and
Pack on myExperiment with semantic
• Trad publications are static
• Electronic documents can be “active”
• Data tables to graphs; protein sequence to structure;
re-run computational workflow within the paper and
• Linking through to a myExperiment pack
• The underpinnings of active documents can be
• Active semantic documents
• Utopia again…
The role of narrative
• Scholarly work needs a narrative
• The narrative carries the argument and the
work conveys a story
• Provides context and evidence
• The message is carried by the narrative
• Data and ontology are both published and
semantic, but lack a narrative
Types of semantic publication
Semantic scholarly publication
• Fulfils these criteria
• But does so enhanced by semantics or is purely
• Rhetorical blocks; semantic types on entities; inter-
and intra-scholarly work semantic relationships; and
• Links out to semantic data and knowledge to
enhance the paper
• Links to semantically described data and ontology
• Make the paper rigorous and consistent
The purely semantic publication
• Can I write a paper only in first order logic?
• Can I come close
• Should I be able to write my paper in logic?
• I can generate the language…
• Can I get in the hedges, probabilities and
scientific weasel words?
• But I could get my hypotheses and conclusion
to match up (Ross King) and I could use
Born or Made?
Made digitalBorn digital
Reference: Becoming Digital: The Challenges of Archiving Digital Photographs,
Karen Rae Simonson, University of Manitoba (Canada), 2006 - 102 pages
Plain to Semantic
• In music recordings we had Analogue (A) and Digital (D)
• Recording, Mastering and Publication as either A or D
• AAA to DDD
• Plain (P) to Semantic (S)
• For the Author, System and Reader
• PPP : Wholly trad Word to PDF; PDF to Word to XML and
PDF; PDF reader…
• Then do it with semantics...
• We need publication process that enable semantics from the
Processes that block having
semantics from the start
It doesn’t take much to give me some
• A DOI gives a type and some computational
• The Kblog story: this is a citation; this is an
ArrayExpress id – I know (and so does a
computer) how to interpret the entity
How much makes me semantic?
• Does one CiTO link a semantic publication summer
• Is a paper semantically born if my authoring tool puts
in ORB or DoCO tags to indicate the rhetorical
• Do I have to have content semantically available?
• Does a link to a semantically tagged myExperiment
pack give a semantic publication?
• A “nanopublication” of the main findings and/or
What’s in it for me?
• Everyone has to get something out of Semantic publishing
• The Lord’s three steps to semantic publishing heaven
• Sepublica 2012
Semantic publication challenges
• Define carefully what is meant by a semantic
publication and set some challenges and boundaries
• Author a born semantic narrative publication
• Topic: Semantic publication (or anything….)
• Make the balance of usefulness for reader and
author reasonable (at this stage we might expect
some work for the author)
• Or just rely on altruism
• Evidence that the semantics help…
Am I any the wiser?
• Judge: I've listened to you for an hour and I'm
none the wiser.
• Smith: None the wiser, perhaps, my lord but
certainly better informed.
• Quoted in "London Letter" by Francis
Cowper in New York Law Journal (28 August
1961), p. 4; also quoted as "Possibly not, My
Lord, but far better informed."
• Sean Bechhofer (for the “Made” and “born”
• Phil Lord
• Bijan Parsia
• Steve Pettifer
• Duncan Hull
• Eleni Mikroyannidi