OBOL Open Biological Ontologies Language

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OBOL - Open Biological Ontologies Language
Chris Mungall
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The OBOL System

• Approach annotation-time term composition vs
  tools for maintenance of large directed acyclic
  graphs
• Requires new generalization hierarchies
• Term decomposition using grammars
• Generating computable logical definitions
• Using logical definitions term creation and
  error checking

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A Formal Grammar for OBO terms

• All GO terms are NOUN-PHRASES
• A NOUN-PHRASE is (recursively) made from
• a NOUN (includes inflected verbs eg binding)
• an ADJECTIVE followed by a NOUN-PHRASE
• a NOUN-PHRASE preceeded by a NOUN-PHRASE acting
  as ADJECTIVE eg clathrin coat
• a NOUN-PHRASE then PREPOSITION then NOUN-PHRASE
  eg regulation of transcription
• an (optional) NOUN-PHRASE then a RELATIONAL
  ADJECTIVE then a NOUN-PHRASE eg clathrin-coated
  vesicle
• Precedence rules are also required to prune parse
  forest

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• ISA927 relationships

• PARTOF186 relationships

holonym
meronym
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Classical Extensional Mereology

• The formal properties of parts
• If A is a proper part of B then B is not a part
  of A (nothing is a proper part of itself)
• If A is a part of B and B is a part of C then A
  is a part of C
• Because of these rules, we can apply some
  functions to parts

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Extensional Mereology (EM) a formal theory of
parts
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Exon distribution to transcripts Drosophila
chromosome 4.
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