Semantic Publishing: What does it all mean anyway?

Robert Stevens

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 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

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”

Amino Acid Ontology

Linked Open Data Cloud

http://richard.cyganiak.de/2007/10/lod/

CiTO: citation typing

Cito: cites as source document

http://www.jbiomedsem.com/content/1/S1/S6

http://getUtopia.comArticle level metrics

Crossref

Sherpa/Romeo

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

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.com/2010/10/14/introducing-the-semantic-publishing-and-referencing-spar-ontologies/

• http://swan.mindinformatics.org/ontology.html

Pack on myExperiment with semantic tags

http://www.myexperiment.org

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…

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 publicationNarrative

Data Knowledge

Desiderata for scholarly publication

• Context/situation

• Evidence

• Argumentation, rhetoric

• Thesis, message,…

• Trustworthiness, provenance, audit trail.

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

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

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

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

Processes that block having semantics from the start

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

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?

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

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."

Acknowledgements

• Sean Bechhofer (for the “Made” and “born” distinction)

• Phil Lord

• Bijan Parsia

• Steve Pettifer

• Duncan Hull

• Eleni Mikroyannidi