Task: Create RDF to describe entries in the NCBI database Online Mendelian Inheritance in Man (OMIM)
- Find and use controlled vocabulary for disease/condition that will enable later linking of different content.
- Generate RDF annotation suitable for linking disease, gene, and papers about the disease, and for gathering into the BioRDF demo.
Participants: Davide Zaccagnini, Chris Mungall?
Use case context: Link to and from information about inherited neurological diseases.
Problem statement for this use case:
In order to bridge the gap from bench to bedside, we need explicitly represented resources that cross the boundary from disease to genetics. OMIM is one such resource, giving information about the disease itself, relating it to known information about genes or loci playing a role in the disease. By linking back to papers in pubmed, a researcher can quickly navigate to the primary source for the information. Major entities that might be made available in RDF from OMIM are gene, chromosome and position within, disease symptoms as freetext, names of populations with different prevalance, and pubmed identifiers.
- Informal proposal of what the content of the RDF will be. Which fields are structured/unstructured. Minimal: Disease name, Gene, chromosome, locus, references to papers.
- Choice of controlled vocabulary/ontology for disease, if feasible.
- Version of RDF suitable for linking gene, chromosome, papers, diseases. To limit the scope we could choose to translate the 1000 or so records retrieved on a search for "neuro".
- List of opportunities for extraction of further information by text mining.
- Any artifacts generated in the process, scripts, spreadsheets etc.
- Lessons learned
- OMIM, a catalog of human genes and genetic disorders.
- Example OMIM Entry in XML, html
- Description of OMIM fields
- Mesh Terms for Mental disorders
- Mesh terms for Central nervous system diseases
- Mesh terms for Central Nervous system anatomy
- OBO Disease ontology
- OBO ontologies in a variety of different formats, including RDF
- Towards a formalization of disease-specific ontologies for neuroinformatics
Task supports and dependencies:
Tools and Services:
Timeline for Task Completion
- Stage 1
- Stage 2