SWAN/SIOC: Aligning Scientific Discourse Representation and Social Semantics Alexandre Passant1, Paolo Ciccarese2, 3, John G. Breslin4, Tim Clark2, 3 1 DERI, NUI Galway, Ireland 2 Massachusetts General Hospital, Boston, USA 3 Harvard Medical School, Boston, USA 4 School of Engineering and Informatics, NUI Galway, Ireland School of Engineering and Informatics

Motivation To provide a complete RDF-based model to model online activities and scientific argumentation in neuromedicine: Combining Web 2.0 shared knowledge using SIOC and formal scientific data (hypotheses, claims, dialogue, evidence, publications, etc.) via SWAN To make (both formal and informal) discourse concepts and relationships more accessible to computation: So that they can be better navigated, compared and understood both across and within domains School of Engineering and Informatics

How is this achieved? An alignment of ontologies was performed to provide a complete framework for modelling activities in scientific communities SWAN objects were integrated into SIOC Types module SWAN was reused to model argumentative discussions External models such as SCOT and MOAT were reused for tagging SCF is being updated so that it can create data according to this model School of Engineering and Informatics

Collaborative websites are like data silos School of Engineering and Informatics * Source: Pidgin Technologies, www.pidgintech.com

Many isolated communities of users and their data School of Engineering and Informatics * Source: Pidgin Technologies, www.pidgintech.com

Need ways to connect these islands School of Engineering and Informatics * Source: Pidgin Technologies, www.pidgintech.com

Allowing users to easily move from one to another School of Engineering and Informatics * Source: Pidgin Technologies, www.pidgintech.com

Enabling users to easily bring their data with them School of Engineering and Informatics * Source: Pidgin Technologies, www.pidgintech.com

Types of data silos (scientific and social) Collaborative websites used by scientific researchers in various domains: SWAN/SCF is being used to connect these Social websites used by people collaborating or communicating through the Web 2.0 platform: SIOC is being used to connect these SWAN/SIOC connects both sets of data silos together, not just structures but what is embedded within content as well School of Engineering and Informatics

SWAN (Semantic Web Applications in Neuromedicine) An ontology of scientific discourse (Ciccarese et al. 2008) A participatory knowledge base of hypotheses, claims, evidence and concepts in biomedicine, with the first instance in the domain of Alzheimer’s disease (AD) Currently being integrated with the SCF (Science Collaboration Framework) toolkit for biomedical web communities http://swan.mindinformatics.org/ School of Engineering and Informatics

What does SWAN consist of? A formal structure to record and present scientific discourse Tools for scientists to manage, access and share knowledge Tools for discovering conflicts, gaps and missing evidence An information bridge to promote collaboration A community process built upon the Alzforum site School of Engineering and Informatics

Main concepts and relationships in the SWAN ontology School of Engineering and Informatics

Modules in the SWAN ontology School of Engineering and Informatics

A typical hypothesis School of Engineering and Informatics

Contributions from leading researchers Key research topics Mechanisms of disease Inventory of ideas Contribute content School of Engineering and Informatics

Computer view Scientist view Knowledge organised for computer processing, integration and reasoning Scientist view Toxic protein fragments believed responsible for AD Key information, gaps and conflicts [Steve - another slide best shown in animation - I have broken it into two slides to make it more readable on printout.] As we said in the previous slide, SWAN’s content is specialized scientific content presented in a way scientists can use. <click to get first animation - slide fades and scientist view is circled>. School of Engineering and Informatics

Browsing evidence and inconsistencies New experiment required? School of Engineering and Informatics

A researcher-supported effort Dozens of etiopathological AD models annotated by SWAN curators in collaboration with leading researchers Content reviewed before release by over twenty senior AD researchers Software features reviewed before release by over thirty senior AD researchers Extensive feedback incorporated into SWAN, such that this is a community tool (in line with Web 2.0 principles) School of Engineering and Informatics

Semantically-Interlinked Online Communities (SIOC) An effort from DERI, NUI Galway to discover how we can create / establish ontologies on the Semantic Web Goal of the SIOC ontology is to address interoperability issues on the (Social) Web http://sioc-project.org/ SIOC has been adopted in a framework of 50 applications or modules deployed on over 400 sites Various domains: Web 2.0, enterprise information integration, HCLS, e-government School of Engineering and Informatics

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The steps taken Develop an ontology of terms for representing rich data from the Social Web Create a food chain for producing, collecting and consuming SIOC data As well dissemination via papers about SIOC, provide docs and examples at sioc-project.org SIOC aims to enrich the Web infrastructure: During the next upgrade cycle, gigabytes of semantically-enriched community data become available! School of Engineering and Informatics

Some of the SIOC core ontology classes and properties School of Engineering and Informatics

Some examples of where SIOC is already use (about 50 applications / modules) School of Engineering and Informatics

Creating a Social Semantic Web of previously-disconnected social “data silos” School of Engineering and Informatics

Also integrating scientific “data silos” in a semantic scientific collaboration framework Enabling researchers to: Collect data Draw conclusions Gather information Create/modify hypotheses Perform experiments But with the benefit of cross- community and cross-domain experiences and results School of Engineering and Informatics

Mappings between SWAN and SIOC at http://rdfs.org/sioc/swan in OWL-DL School of Engineering and Informatics

Mappings between SWAN and SIOC classes Subclasses of sioc:Item: swanscidis:DiscourseElement swanscidis:ResearchStatement swanscidis:ResearchQuestion swanscidis:ResearchComment swancit:Citation swancit:JournalArticle Other mappings: sioc:Post > swancit:WebArticle, swancit:WebNews sioc:Comment > swancit:WebComment swanscidis is the Scientific Discourse module, which provides a set of classes and properties to represent discourse elements swancit is the Citations module, which aims to model the various citation elements that occur in scientific publishing School of Engineering and Informatics

Mappings between SWAN and SIOC properties Subtypes of sioc:related_to: swandisrel:agreesWith / swandisrel:disagreesWith swandisrel:alternativeTo swandisrel:arisesFrom swandisrel:cites swandisrel:consistentWith / swandisrel:inconsistentWith swandisrel:discusses swandisrel:inResponseTo swandisrel:motivatedBy swandisrel:refersTo swandisrel is the Scientific Discourse Relationships module, which collects some of the relationships used for modelling discourse May also use sioc:Item dcterms:hasPart swanscidis:DiscourseElement, for example, to represent that a particular hypothesis is part of a blog post School of Engineering and Informatics

Mappings redundancy Redundant mappings: Can be entailed thanks to the transitivity of rdfs:subClassOf / rdfs:subPropertyOf e.g. “swancit:JournalArticle rdfs:subClassOf sioc:item” can be inferred from “swancit:JournalArticle rdfs:subClassOf swancit:Citation” and “swancit:Citation rdfs:subClassOf sioc:Item” However: SIOC applications generally do not support such chained entailments Need to address lightweight inference Therefore we provide direct rdfs:subClassOf mappings School of Engineering and Informatics

Querying mappings Simple query to identify relatedness between items: PREFIX sioc: <http://rdfs.org/sioc/ns#> SELECT DISTINCT ?s ?o WHERE { ?s sioc:related_to ?o . ?s a sioc:Item . ?o a sioc:Item . } Simple query to identify relatedness between items: Applying a SIOC query over SWAN data SPARQL / Pellet, files loaded on runtime in memory Experiment with both simple mappings (including transitive closure) and full mappings School of Engineering and Informatics

W3C HCLS Interest Group notes published http://www.w3.org/TR/hcls-sioc/ http://www.w3.org/TR/hcls-swan/ http://www.w3.org/TR/hcls-swansioc/ School of Engineering and Informatics

RDFa support in Drupal 7 for SSW data School of Engineering and Informatics

Exposing scientific results to search Yahoo! Search Monkey and Google Rich Snippets Highlights the structured data embedded in web pages Google developers have indicated that scholarly publications marked up with Rich Snippets will also be picked up and appropriately indexed by Google Scholar School of Engineering and Informatics

Acknowledgements We would like to thank Science Foundation Ireland for their support under grant SFI/08/CE/I1380 (Líon 2) We would also like to thank an anonymous foundation for a generous gift in support of this work Thanks to members of the W3C HCLSIG, in particular: Susie Stephens Scott Marshall Eric Prud’hommeaux School of Engineering and Informatics

Motivation To provide a complete RDF-based model to model online activities and scientific argumentation in neuromedicine: Combining Web 2.0 shared knowledge using SIOC and formal scientific data (hypotheses, claims, dialogue, evidence, publications, etc.) via SWAN To make (both formal and informal) discourse concepts and relationships more accessible to computation: So that they can be better navigated, compared and understood both across and within domains School of Engineering and Informatics