Mouse BIRN: Ontologies

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Mouse BIRN Ontologies
Ontology Mark-Up Workshop

• Maryann Martone
• and
• Bill Bug

January 26-27, 2006
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Agenda

• Day 1
• Introduction of participants
• Welcome remarks (Maryann Martone)
• Mapping concepts to knowledge sources (Jeff
  Grethe)
• Identify cross-test bed query
• BIRN Mediator (Vadim)
• Work, work, work!
• Day 2
• AM Work, work, work!
• PM Answer cross test bed query
• Provide feedback on user interface for BIRN
  mediator

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Use of Ontologies in BIRN

• Databases
• Enforces semantic consistency within a database
• Data Sharing
• Establishes semantic relationship among concepts
  contained in distributed databases
• Data integration
• Bridging across multiscale and multimodal data
• Concept-based queries
• Ontologies can be used to alter semantic context
  to present a view of the conceptual aspects of a
  data set or meta-analysis result most relevant to
  a particular neuroscientist

Make BIRN databases and data understandable to
human and machine!
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Goals

• To map databases to BIRN knowledge sources
  (Bonfire) and provide this mapping to BIRN
  mediator
• What should be mapped?
• Table names
• Field (column) names
• Data values
• To extend knowledge bases where necessary to
  accommodate BIRN data
• Add concepts and link them to existing concepts
• Identify areas of difficulty and confusion and
  try to come to consensus
• To identify the set of ontologies currently used
  by BIRN to be added to Bonfire, e.g., NCBI
  taxonomy
• To identify areas that are poorly covered where
  additional ontologies may be needed
• To develop Policies and Procedures for working
  with ontologies in BIRN

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What should be mapped?

• Tables, fields (columns), data
• Project, experiment, subject, technique
• What data?
• What data were measured, recorded or captured and
  by what methods?
• What type of experimental subject was studied?
• What was the design/purpose of the experiment?
• What methods were used to prepare the subject?
• What part of the subject (anatomy, cell Type etc)
  was observed, recorded or altered?
• Courtesy of Dan Gardner, Neuroinformatics
  Framework

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CCDB Dictionary
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Will this be easy and straightforward?

• No
• Mappers will encounter difficulties, some of
  which will have a good answer, some of which will
  have an acceptable answer and some of which will
  have no answer
• Bring problems to the group!

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Deliverables/Benchmarks

• concepts mapped
• concepts added
• policies and procedures regarding terminologies
  formalized
• existing ontologies/terminologies of use to
  BIRN identified
• Test queries answered