School of Engineering and Informatics SWAN/SIOC: Aligning Scientific Discourse Representation and Social Semantics Alexandre Passant 1 , Paolo Ciccarese 2, 3 , John G. Breslin 4 , Tim Clark 2, 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
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SWAN/SIOC: Aligning Scientific Discourse Representation and Social Semantics
Semantic Web Applications in Scientific Discourse Workshop at the International Semantic Web Conference / Washington, DC / 26th October 2009
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School of Engineering and Informatics
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
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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
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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
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Collaborative websites are like data silos
* Source: Pidgin Technologies, www.pidgintech.com
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Many isolated communities of users and their data
* Source: Pidgin Technologies, www.pidgintech.com
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Need ways to connect these islands
* Source: Pidgin Technologies, www.pidgintech.com
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Allowing users to easily move from one to another
* Source: Pidgin Technologies, www.pidgintech.com
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Enabling users to easily bring their data with them
* Source: Pidgin Technologies, www.pidgintech.com
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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
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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/
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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
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Main concepts and relationships in the SWAN ontology
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Modules in the SWAN ontology
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A typical hypothesis
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Contributions from leading researchers
Key research topics
Contribute content
Inventory of ideas
Mechanisms of disease
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Scientist viewToxic protein fragments believed responsible for AD
Key information, gaps and conflicts
Computer viewKnowledge organised for
computer processing, integration and reasoning
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Browsing evidence and inconsistencies
New experiment required?
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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)
• 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
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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
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Querying mappings
• 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
PREFIX sioc: <http://rdfs.org/sioc/ns#>SELECT DISTINCT ?s ?oWHERE {?s sioc:related_to ?o .?s a sioc:Item . ?o a sioc:Item .}
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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/
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RDFa support in Drupal 7 for SSW data
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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
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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
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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