Biomedical Informatics Research Network (BIRN)
Maryann Martone, NCMIR, University of California, San Diego
The University of California, San Diego, collaborative R01 is developing a phenotype ontology for neurodegenerative disease as part of the Mouse BIRN network. The BIRN is a national center for research resources, with a cyberinfrastructure for storing, manipulating and sharing data and resources. Current BIRN test beds focus on neuroscience and neuroimaging, specifically human MRI and fMIR, and mouse models of neurological disease.
UCSD's National Center for Microscopy and Imaging Research (NCMIR) supplies high resolution light and electron microscopic data on mouse models of neurodegenerative disease for the Mouse BIRN. They have developed an on-line database, the Cell Centered Database, and a Subcellular Anatomy Ontology (SAO), which is searchable in the OBO foundry.
NCMIR uses the SAO and Jinx to annotate segmentations of their 3D electron microscopic image data. Additionally, NCMIR contributes large scale brain mosaics to the mouse BIRN, which they register to the common coordinate system established for the mouse brain, using a set of tools developed by BIRN collectively called Smart Atlas.
As one of the major objectives of BIRN is to compare animal models to human disorders, this R01 is working with NCBO to annotate their mouse model neuroimages with phenotype statements using PATO via Phenote+. In testing the utilization of PATO for phenotype annotation, NCMIR is establishing templates and tools to be used by other BIRN participants. NCMIR is also working with BIRN to align their data mediation environment more closely with the BioPortal and RDF/OWL ontologies. To see an example of their work, please see here.
Specific goals for this project include:
- Capture phenotypes across neurodegenerative diseases to look for underlying commonalities and differences in both human conditions and in animal models of these disorders.
- Develop an intuitive ontology-based environment for annotation of spatially and temporally varying phenotypes contained in multiscale images
- Extend the current BIRN Federated Data Integration Environment to be compatible with ontology tools/data coming from NCBO, in order to compare animals models with human disorders.
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