applying the semantic web at uchsc - center for computational pharmacology ian wilson
TRANSCRIPT
Applying the Semantic Web at UCHSC - Center for Computational Pharmacology
Ian Wilson
Projects with semantics at UCHSC-CCP Integrated Neuroscience Initiative on
Alcoholism (INIA) Analysis Suite Ongoing project to support the INIA
consortium (30+ universities geographically dispersed)
First release at the Neuroscience 2004 conference – Microarrays only at the moment
NLP Enrichment Opportunities Recent funding September 2004 – NLM
Data integration framework for life science knowledge-bases
INIA SemWeb Opportunities Conversion of LISP-CM based signal
transduction knowledge-base to OWL Application framework to link the semantics
of our data – e.g. MAGE, fMRI, etc. Exploring ‘scientific workflow’ tools to
enable composition of semantically annotated web services – easy UI for the investigator myGrid project – also presenting at the
conference Issues with the granularity of semantics
NLP Enrichment Opportunities Using Direct Memory Access Parsing
(DMAP) – ‘conceptual parsing’ supported by ontologies
Developing Protege plug-in to support NLP annotations – gold standard development
Text sources Entrez GeneRIFs
255 character summary of gene function derived from PubMed
Gene Ontology Definitions
Data Integration Framework Creating RDF wrappers for several
bioinformatics data sources Using NCBI, GO, Uniprot, etc. as test cases Alignment of several bio-ontologies –
extending when appropriate Investigating/benchmarking several
triple stores and browsers Kowari, Jena, Sesame Lightweight JSP, Longwell
Mappings are not always straight forward
Why integrate? Current architecture is not maintainable
Web tiered databases Data models in flux Web client interfaces in flux Everyone has a different client interface and data model design
CLI tools
500+ services/databases & Growing
Cutting and pasting
Large number of steps
Frequently repeated – info now rapidly added to public databases
Don’t always get results
Semantic Web Concerns Inference
Modeling default reasoning and negation in OWL?
Reification is not sufficient for context – Quads Named graphs
DL’s are good for certain tasks, but Need other logics in the life sciences closed world reasoning – e.g. rules
Scalability Need to constrain search in RDF space
Conclusion
Always looking for collaborators Questions?