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Setting Normative Function: Describing Phenotype
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Setting Normative Function: Describing Phenotype

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The ability to unambiguously describe phenotypes for all human disease in a manner that is able to be used and understood by both humans and computers is a challenge that cuts across the entire Human …

The ability to unambiguously describe phenotypes for all human disease in a manner that is able to be used and understood by both humans and computers is a challenge that cuts across the entire Human Variome Project. This presentation was used as a discussion starter for the "Describing Phenotype" session at the 4th Biennial Meeting of the Human Variome Project Consortium. These session discussed the logistics of collection and reporting of phenotype, how phenotypes can be validated, as well as the ethics of reporting phenotype on publicly accessible databases.

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  • 1. HVP Phenotype Session Audience discussion Five slides with suggested/potential topics
  • 2. Phenotype Databases What can be achieved by databases with goodphenotype data? What kind of phenotype data needs to go in? Role of specialised vs. „universal“ database? Advantages of phenotype-centric, (single-) genecentric, or exome/genome-centric databases?
  • 3. Standards/Terminologies/Ontologies Disease nosology, phenotypic features,...,? How many ontologies are optimal? How to ensure interoperability between ontologies? How to relate specialist ontologies to hospital ITsystems such as SNOMED-CT? Should we map legacy data? Who does the biocuration? Who pays for it?
  • 4. Quality control of Phenotype Data How to ensure good quality data goes in? How to motivate physicians and others to enterhigh-quality and complete phenotype data? How to check for quality and completeness ofphenotype data in databases?
  • 5. Technical Standards for Phenotype Data How to ensure interoperability of databases? Role for Semantic Web technologies? Other technologies for standardised data exchange? What needs to be done to connect hospitals andresearch labs to the rest of the network to transmit data? Who manages researcher identities for access control?
  • 6. Data Access & Administration Who is allowed access to phenotype data (whichin combination with genotypes raises issues ofidentifiability)? The MD? The patient? All registered reseachers? The  world? Where should the data „live“?  Centralized vs. Federated databases? Sustainability?
  • 7. Ethics of Phenotype Databasing Do we need special consent for Web phenotypedatabases? What about vulnerable persons (e.g., ID)? Optimal makeup of ethics oversight committees? Do we need to rethink our notions of Privacy inthis Facebook-era?
  • 8. Phenotype Workshop at the ASHG Getting Ready for The Human Phenome Project ASHG Satellite, San Francisco Tuesday 6th November 2012,  8.30 AM to 3.45 PM Open for abstracts