Applying the Semantic Web at UCHSC - Center for Computational Pharmacology Ian Wilson.
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Transcript of Applying the Semantic Web at UCHSC - Center for Computational Pharmacology Ian Wilson.
![Page 1: Applying the Semantic Web at UCHSC - Center for Computational Pharmacology Ian Wilson.](https://reader036.fdocuments.in/reader036/viewer/2022082422/56649e8e5503460f94b91133/html5/thumbnails/1.jpg)
Applying the Semantic Web at UCHSC - Center for Computational Pharmacology
Ian Wilson
![Page 2: Applying the Semantic Web at UCHSC - Center for Computational Pharmacology Ian Wilson.](https://reader036.fdocuments.in/reader036/viewer/2022082422/56649e8e5503460f94b91133/html5/thumbnails/2.jpg)
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
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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
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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
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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
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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
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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
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Conclusion
Always looking for collaborators Questions?