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shared phenotype ontology

general consensus for PATO

ontologies that describe time

development, evolution

overall ontology for anatomy, to include "homology" concept

  • all biologists really want, but philosophers can't operationalize it
  • groups of organisms with major transitions especially want this



whole-organism process ontologies

  • processes: events that occur in space and time
  • vocabulary for function of those processes

Missing Features of Annotation Tools

  • "use common ontologies"
  • multi-user support
  • "access annnotation DB"
  • ease of finding terms
  • support for standards
  • "proofing of annotations"

links and sources

omniscan -- associative access to everything

Missing features of ontology development tools

  • tools that facilitate alignment of ontologies
  • support collaborative development
  • support consistency checks
  • support higher-order relations
  • support multiple ontology editing
  • tools to facilitate term extraction from text
  • tools to help identify synonymous terms

ontology request broker

  • a glue technology
  • request term, get receipt (temporary term)
  • update later
  • comment (Monte): gatekeepers

lack of standards

  • proliferation of standards
  • basis for interoperability is semantic or structured information

driving questions or grand challenges

  • provide common focus and motivations for many phenotype-related projects
  • change focus from individual projects to grand challenges
  • would bring many phenotype issues to one question

coding phylogenetic data

  • how to encode them as character data
  • tools to identify components of phylogenetic data
  • agree on the standards or the process for encoding data in characters

cross-database phenotype searching (phenoblast)

  • similarity searches based on phenotypes
  • tool relates to grand challenge

best practices for developing ontologies

  • quality-control standards

killer app

  • demonstration of utility (of ontological data & reasoning) to biologists
  • doing it at different educational levels
  • bring reasoning & ontologies more into training experience

shortage of skilled manpower

  • training

recruiting from the community

  • explain what ontologies are
  • provide examples of tangible benefits


  • reward system to motivate people to become part of ontology community
  • citation ratings for making papers easily annotated
  • get journals to buy in to ontologies, require term submissions
  • has to count for promotion & tenure