PATO Meeting

General Information and Registration

The National Center for Biomedical Ontology will host a two-day meeting focused on the Phenotype and Trait Ontology (PATO) December 1-2, 2006 at Stanford University in Palo Alto, CA.

Register here.

Venue

Stanford University Clark Center, room S360

Directions to Stanford Medical Center

Map of Stanford Medical Center--see "C", Clark Center

Directions on taking Free Marguerite Shuttle Bus--take Line A to Medical Center

Accommodations

We aren't reserving a block of rooms anywhere, but these local hotels are close by and have Stanford shuttle service.

Draft agenda

Thursday, November 30, 2006
- 7pm: Informal gathering for dinner (Gordon Biersch?)

Friday, December 1, 2006
- 8:30 - 5:30pm Meeting
  - Introduction to PaTO
  - Phenote
  - Discussion of correlating pre-coordinated phenotype ontologies (such as: MP, plant_trait) with E-Q (Entity-Quality) ontologies (such as: various anatomies and PaTO).

Saturday, December 2, 2006
- 8:30 - 5:30pm Meeting

Abstracts for Presentations

PaTO: An Introduction (Suzanna Lewis)

Abstract: This is simply an introduction to PaTO, to bring people up to speed on its current status.

Challenges for Representing Phenotype in Pharmacogenomics (Russ Altman)

Abstract: The PharmGKB (http://www.pharmgkb.org/) is an online resource devoted to comprehensive cataloguing of genetic variations relevant to variation in drug response. We curate primary data (genotype, phenotype at molecular, cellular, clinical level) as well as knowledge (literature curation, pathways, human annotations of key genes). We provide search and visualization tools for this information, in order to catalyze research in pharmacogenomics. For both activities, we need to index the relevant phenotypes for the purposes of indexing, aggregation, search, and automatic summarization and data mining. We need a flexible method for annotating phenotypes that are described in the literature (by curators). We would prefer to adopt community-based standards that would allow PharmGKB to interoperate with other databases, both human and model organism.

Ontologies and Vocabularies Supporting Data Integration: Emphasis on Mouse Phenotypes and Disease (Janan Eppig)

Abstract: The mouse is an exceptional model system for connecting knowledge from sequence-to-phenotype-to-disease. The Mouse Genome Informatics Database (MGI, http://www.informatics.jax.org) supports biological knowledge building for mouse by integrating genetic, genomic, and biological data and facilitating data mining and complex querying. Full access to integrated data is enabled by extensive use of structured vocabularies and ontologies including the Gene Ontology (GO), mouse Embryonic and Adult Anatomical Dictionaries (EMAP and MA), Mammalian Phenotype (MP) Ontology, and Online Mendelian Inheritance in Man (OMIM) disease and syndrome terms. In addition, MGI is the authoritative source for nomenclature for mouse genes, alleles, and strains. Many smaller vocabularies, such as mutation class, sequence type, genetic marker type, expression assay type, etc., also are key to MGI data integration. Phenotypic descriptions in MGI rely on the MP Ontology and definition of specific genotypes and strain backgrounds. The MP Ontology has been adopted successfully to describe mouse (MGI), rat (RGD), human (NBCI), and animal (OMIA) phenotypes. As of July 2006, MGI included >16,000 alleles representing phenotypic mutations in >6,600 genes. Over 65,600 phenotype annotations in MGI have been made using MP Ontology terms. The MP Ontology itself has, thus far, grown to >4,400 defined terms. Over 1,700 mouse models are associated with OMIM disease terms. Supported by NIH grant HG00330.

Rat Genome Database Disease Portals: A Platform for Genetic and Genomic Research (Victoria Petri)

Abstract: The Disease Portals at RGD provide a comprehensive research platform through the integration of heterogeneous datasets into the context of the genome using multiple ontologies and tools for data mining and visualization. The portals provide both the novice/experienced user with easy access to a comprehensive, integrated knowledgebase. Current/proposed components of the portals include: 1) comprehensive rat, human and mouse gene sets associated with diseases, related phenotypes, pathways and biological processes; 2) all rat QTLs related to a disease, associated mouse/human QTLs; 3) strains used as disease models; 4) phenotype data in a species-dependent manner; 5) references; 6) expression data; 7) genome-wide view of genes/QTLs via GViewer; 8) comparative maps of disease related regions, 10) customization of datasets/download options; 11) analysis/visualization of function and cellular localization makeup of gene sets. The portals are designed to highlight genetic/ genomic data generated from rat research in diseases related to the cardiovascular, nervous, musculoskeletal, digestive, endocrine and immune systems as well as metabolic diseases, cancer. Disease data across the three species, along with species-dependent phenotypic data provide the user with a means to distinguish between subtle differences in disease manifestations. Such differences could help elucidate the links between events and conditions, the mechanisms that lead from the normal to the diseased phenotype.