Sepublica 2012 keynote

1. Semantic Publishing:
What does it all mean anyway?
Robert Stevens
University of Manchester, UK

2. So, what am I going to do?
• Define some terms
• Pose lots of questions
• Introduce some concepts
• Set some Challenges
• Solve semantic publication

3. First catch your terms
• Publication: Exposure to the public (sic) OF SOME
AUTHORED WORK
• Publication – the process (the act) and the published
thing
• Semantic: capturing the meaning of information in
some computationally amenable form
• Authoring: The process of “WRITING” some WORK
• Semantic Web: The Web plus computational
meaning
• Things on the Web are published

4. Semantic publication
• A publication enhanced with semantics
• We usually think of a publication as an article – some
scholarly work
• 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
Web
• 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”

5. Amino Acid Ontology

6. Linked Open Data Cloud
http://richard.cyganiak.de/2007/10/lod/

7. CiTO: citation typing
Cito: cites as source document
http://www.jbiomedsem.com/content/1/S1/S6

8. http://getUtopia.com
Article level metrics
Crossref
Sherpa/Romeo

9. Post processing of articles with text
mining and NLP
• Marking up entities with text mining
• Named entity recognisers for different types of
entity
• Normalised to identifiers – could add
semantics and other TM to give relationships
• AO and all that

10. Embedding semantics into scholarly
articles
• But I could do all of this from the
start if my tools were good
enough
• Methods and data might be the
easiest to make semantic from
the start
• Even “easier” would be
rhetorical blocks and
citation/bibliographic structures
• http://opencitations.wordpress.c
om/2010/10/14/introducing-the-
semantic-publishing-and-
referencing-spar-ontologies/
• http://swan.mindinformatics.org/
ontology.html

11. Pack on myExperiment with semantic
tags
http://www.myexperiment.org

12. Active documents
• 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
so on
• Linking through to a myExperiment pack
• The underpinnings of active documents can be
semantic
• Active semantic documents
• Utopia again…

13. 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

14. Types of semantic publication
Narrative
Data
Knowledge

15. Desiderata for scholarly publication
• Context/situation
• Evidence
• Argumentation, rhetoric
• Thesis, message,…
• Trustworthiness, provenance, audit trail.

16. Semantic scholarly publication
• Fulfils these criteria
• But does so enhanced by semantics or is purely
semantic
• Rhetorical blocks; semantic types on entities; inter-
and intra-scholarly work semantic relationships; and
so on
• Links out to semantic data and knowledge to
enhance the paper
• Links to semantically described data and ontology
publications
• Make the paper rigorous and consistent

17. 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
consistent vocabulary

18. Born or Made?
Made digitalBorn digital
Born semantic
Made semantic
Reference: Becoming Digital: The Challenges of Archiving Digital Photographs,
Karen Rae Simonson, University of Manitoba (Canada), 2006 - 102 pages

19. 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
start

20. Processes that block having
semantics from the start

21. It doesn’t take much to give me some
semantics
• A DOI gives a type and some computational
amenability...
• The Kblog story: this is a citation; this is an
ArrayExpress id – I know (and so does a
computer) how to interpret the entity

22. How much makes me semantic?
• Does one CiTO link a semantic publication summer
make?
• Is a paper semantically born if my authoring tool puts
in ORB or DoCO tags to indicate the rhetorical
structure?
• 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
conclusions?

23. What’s in it for me?
Author
System Reader
Semantic
publishing
heaven
• Everyone has to get something out of Semantic publishing
• The Lord’s three steps to semantic publishing heaven
• Sepublica 2012

24. 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…

25. 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."

26. Acknowledgements
• Sean Bechhofer (for the “Made” and “born”
distinction)
• Phil Lord
• Bijan Parsia
• Steve Pettifer
• Duncan Hull
• Eleni Mikroyannidi