SWAT4LS2009 – Keynote Alan Ruttenberg: Semantic Web Technology to Support Studying the Relation of HLA Structure Variation to Disease

(These are live-blogging notes from Alan’s keynote…so don’t expect any coherent text….use them as bullt points to follow the gist of the argument.)

The Science Commons:

• a project of the Creative Commons
• 6 people
• CC specializes CC to science
• information discovery and re-use
• establish legal clarity around data sharing and encourage automated attribution and provenance

Semantic Web for Biologist because it maximizes value o scientific work by removing repeat experimentation.

ImmPort Semantic Integration Feasibility Project

• Immport is an immunology database and analysis portal
• Goals:metaanalysis
• Question: how can ontology help data integration for data from many sources

Using semantics to help integrate sequence features of HLA with disorders
Challenges:

• Curation of sequence features
• Linking to disorders
• Associating allele sequences with peptide structures with nomenclature with secondary structure with human phenotype etc etc etc…

Talks about elements of representation

• pdb structures translated into ontology-bases respresentations
• canonical MHC molecule instances constructed from IMGT
• relate each residue in pdb to the canonical residue if exists
• use existing ontologies
• contact points between peptide and other chains computed using JMOL following IMGT. Represented as relation between residue instances.
• Structural features have fiat parts

Connecting Allele Names to Disease Names

• use papers as join factors: papers mention both disease and allele – noisy
• use regex and rewrites applied to titles and abstracts to fish out links between diseases and alleles

Correspondence of molecules with allele structures is difficult.

• use blast to fiind closest allele match between pdb and allele sequence
• every pdb and allele residue has URI
• relate matching molecules
• relate each allele residue to the canonical allele
• annotate various residoes with various coordinate systems

This creates massive map that can be navigated and queried. Example queries:

• What autoimmune diseases can de indexed against a given allele?
• What are the variant residues at a position?
• Classification of amino acids
• Show alleles perturned at contacts of 1AGB

Summary of Progress to Date:
Elements of Approach in Place: Structure, Variation, transfer of annotation via alignment, information extraction from literature etc…

Nuts and Bolts:

• Primary source
• Local copy of souce
• Scripts transforms to RDF
• Exports RDF Bundles
• Get selected RDF Bundles and load into triple store

• Parsers generate in memory structures (python, java)
• Template files are instructions to fomat these into owl
• Modeling is iteratively refined by editiing templates
• RDF loaded into Neurocommons, some amount of reasoning

RDFHerd package management for data

neurocommons.org/bundles

Can we reduce the burden of data integration?

• Too many people are doing data integration – wasting effort
• Use web as platform
• Too many ontologies…here’s the social pressure again

Challenges

• have lawyers bless every bit of data integration
• reasoning over triple stores
• SPARQL over HTTP
• Understand and exploit ontology and reasoning
• Grow a software ecosystem like Firefox