Semantically enabling a genome-wide association study database by Tim Beck, Robert C Free, Gudmundur A Thorisson and Anthony J Brookes. Journal of Biomedical Semantics 2012, 3:9 doi:10.1186/2041-1480-3-9.
Abstract:
Background
The amount of data generated from genome-wide association studies (GWAS) has grown rapidly, but considerations for GWAS phenotype data reuse and interchange have not kept pace. This impacts on the work of GWAS Central — a free and open access resource for the advanced querying and comparison of summary-level genetic association data. The benefits of employing ontologies for standardising and structuring data are widely accepted. The complex spectrum of observed human phenotypes (and traits), and the requirement for cross-species phenotype comparisons, calls for reflection on the most appropriate solution for the organisation of human phenotype data. The Semantic Web provides standards for the possibility of further integration of GWAS data and the ability to contribute to the web of Linked Data.
Results
A pragmatic consideration when applying phenotype ontologies to GWAS data is the ability to retrieve all data, at the most granular level possible, from querying a single ontology graph. We found the Medical Subject Headings (MeSH) terminology suitable for describing all traits (diseases and medical signs and symptoms) at various levels of granularity and the Human Phenotype Ontology (HPO) most suitable for describing phenotypic abnormalities (medical signs and symptoms) at the most granular level. Diseases within MeSH are mapped to HPO to infer the phenotypic abnormalities associated with diseases. Building on the rich semantic phenotype annotation layer, we are able to make cross-species phenotype comparisons and publish a core subset of GWAS data as RDF nanopublications.
Conclusions
We present a methodology for applying phenotype annotations to a comprehensive genome-wide association dataset and for ensuring compatibility with the Semantic Web. The annotations are used to assist with cross-species genotype and phenotype comparisons. However, further processing and deconstructions of terms may be required to facilitate automatic phenotype comparisons. The provision of GWAS nanopublications enables a new dimension for exploring GWAS data, by way of intrinsic links to related data resources within the Linked Data web. The value of such annotation and integration will grow as more biomedical resources adopt the standards of the Semantic Web.
Rather than:
The benefits of employing ontologies for standardising and structuring data are widely accepted.
I would rephrase that to read:
The benefits and limitations of employing ontologies for standardising and structuring data are widely known.
Decades of use of relational database schemas, informal equivalents of ontologies, leave no doubt governing structures for data have benefits.
Less often acknowledged is those same governing structures impose limitations on data and what may be represented.
That’s not a dig at relational databases.
Just an observation that ontologies and their equivalents aren’t unalloyed precious metals.