HCLSIG Demo Proposals

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Demonstration scenarios that have been proposed by members of the HCLSIG

Demo from the Amsterdam F2F meeting

(rough consensus of the participants of the Amsterdam F2F at the time of the meeting)

Demonstrates: Description of multi-level information from neuroscience, more on the bench- than on the bedside. Interaction of pharmacological substances with receptors, receptor-distribution, annotation of pharmacological substances with MeSH.

Existing assets: Senselab/NeuronDB, PDSP Ki DB, MeSH in OWL. Parkinson’s Disease ontology (however it was unclear at the time how the Parkinson’s ontology should interact with the BioRDF datasets).

I have summarized the status of this demo some months ago; I think not much has changed since then: http://www.mail-archive.com/public-semweb-lifesci@w3.org/msg01380.html

Alzheimer’s Disease Immunotherapy Scenario

(described in the final version of the paper submitted to BMC Bioinformatics, strongly influenced by the members of Alzforum)

Demonstrates: queries similar to the Parkinson’s disease use-case, also including antibody databases.

Existing assets: BrainPharm, Alzforum Antibody database.

bio-zen / POMR demo

(proposed by Matthias Samwald)

Links: http://neuroscientific.net/res/semsyn/bio-zen-demo/bio-zen-demo.htm http://esw.w3.org/topic/MatthiasSamwald/DOLCE_bio-zen_patient-record_proposal http://esw.w3.org/topic/HCLS/POMROntology

Demonstrates: application in basic research and clinical records, bench-to-bedside transition, integration of external vocabularies and taxonomies, ontology-based resource resolution and management of digital resources, foundational ontologies and metadata standards, information ecosystem / publishing / hypothesis formulation, copyright management and integration into web applications (e.g. Semantic Wikis).

Existing assets: bio-zen ontology, POMR ontology, OBO taxonomies converted to SKOS / bio-zen, datasets converted from databases available in BioPAX format (including KiDB and BIND that have been converted as part of BioRDF), third-party software written for the integrated ontologies like FOAF or SKOS.

BIRN / imaging demo

(proposed by Bill Bug and others during teleconferences)

Demonstrates: semantic integration of imaging data (e.g. to discover meaningful colocalizations in space and time).

Existing assets: BIRN resources (how much of these resources are already in a usable RDF/OWL format)

Demo for self-publishing experiment ontology and tools

(proposed by AJ Chen)

http://www.mail-archive.com/public-semweb-lifesci@w3.org/msg01137.html http://esw.w3.org/topic/HCLS/ScientificPublishingTaskForce

Demonstrates: (1) adding a simple layer of semantic annotation to wordpress blogger software to facilitate self-publishing of experiment data; (2) searching of the published semantic data on a community search engine.

Existing assets: AJ Chen's open project demo site for publishing tool and search engine.