obo-schema

Obo-Schema schema

A high level map of OBO classes and how they connect

Classes

• AbnormalPhenotype
  • SpeciesNeutralAbnormalPhenotype
  • SpeciesSpecificAbnormalPhenotype
• AtomicTraitOrPhenotypicFeature
  • AtomicPhenotypicFeature
    • AnatomicalAtomicPhenotypicFeature
    • BiologicalProcessAtomicPhenotypicFeature
    • ChemicalEntityAtomicPhenotypicFeature
  • AtomicTrait
• Characteristic
  • CharacteristicAttribute
  • CharacteristicValue
• Disease
• Entity
  • PhysicalEntityOrProcess
    • Occurrent
      • LifeStage
        • SpeciesNeutralLifeStage
        • SpeciesSpecificLifeStage
    • PhysicalEntity
      • AnatomicalEntity
        • AbormalAnatomicalEntity
        • ConstructedCellType
        • EvolvedAnatomicalEntity
          • CellularEvolvedAnatomicalEntity
          • EvolvedCellType
            • SpeciesNeutralEvolvedCellType
            • SpeciesSpecificEvolvedCellType
          • GrossEvolvedAnatomicalEntity
            • SpeciesNeutralGrossEvolvedAnatomicalEntity
            • SpeciesSpecificGrossEvolvedAnatomicalEntity
        • GrossConstructedAnatomicalEntity
        • GrossPathologicalAnatomicalEntity
        • PathologicalCellType
        • VariantAnatomicalEntity
      • ChemicalEntity
      • PlanetaryEntity
    • Process
      • BiologicalProcessOrMolecularActivity
        • BiologicalProcess
        • MolecularActivity
      • EnvironmentalProcess
      • Exposure
      • PathologicalProcess
• Information
  • OntologyAxiom
  • Publication
• MixtureOfChemicalEntities
  • Food
• OrganismTaxon
  • BroadOrganismTaxon
  • Species
• Unit

Mixins

• Abnormal
• Constructed
• Evolved
• NonOrganismal - an entity or class that is not a part or derived from an organism.
• Organismal
  • SpeciesNeutral - may still be specific to a broader taxonomic grouping, e.g. metazoa. Must explicitly group other ontologies
  • SpeciesSpecific - species specific may also be applicable at broader levels, e.g. genus
• Origin
  • Abnormal
  • Constructed
  • Evolved
  • Variant
• SpeciesNeutral - may still be specific to a broader taxonomic grouping, e.g. metazoa. Must explicitly group other ontologies
• SpeciesSpecific - species specific may also be applicable at broader levels, e.g. genus

Slots

• analog of
  • constructed cell type➞analog of
  • gross constructed anatomical entity➞analog of
  • pathological cell type➞analog of
• characteristic of
  • atomic phenotypic feature➞characteristic of
    • anatomical atomic phenotypic feature➞characteristic of
    • biological process atomic phenotypic feature➞characteristic of
    • chemical entity atomic phenotypic feature➞characteristic of
  • atomic trait➞characteristic of
• develops from
  • anatomical entity➞develops from
    • evolved anatomical entity➞develops from
      • evolved cell type➞develops from
        • species neutral evolved cell type➞develops from
        • species specific evolved cell type➞develops from
      • gross evolved anatomical entity➞develops from
        • species neutral gross evolved anatomical entity➞develops from
        • species specific gross evolved anatomical entity➞develops from
• existence ends during
  • anatomical entity➞existence ends during
    • species neutral evolved cell type➞existence ends during
    • species neutral gross evolved anatomical entity➞existence ends during
    • species specific evolved cell type➞existence ends during
    • species specific gross evolved anatomical entity➞existence ends during
• existence starts during
  • anatomical entity➞existence starts during
    • species neutral evolved cell type➞existence starts during
    • species neutral gross evolved anatomical entity➞existence starts during
    • species specific evolved cell type➞existence starts during
    • species specific gross evolved anatomical entity➞existence starts during
• has part
  • abnormal phenotype➞has part
  • mixture of chemical entities➞has part
• in taxon
  • organismal➞in taxon
    • species neutral➞in taxon
    • species specific➞in taxon
• never in taxon
  • organismal➞never in taxon
• part of
  • anatomical entity➞part of
    • constructed cell type➞part of
    • evolved anatomical entity➞part of
      • cellular evolved anatomical entity➞part of
      • evolved cell type➞part of
        • species neutral evolved cell type➞part of
        • species specific evolved cell type➞part of
      • gross evolved anatomical entity➞part of
        • species neutral gross evolved anatomical entity➞part of
        • species specific gross evolved anatomical entity➞part of
    • gross constructed anatomical entity➞part of
    • gross pathological anatomical entity➞part of
    • pathological cell type➞part of
• part_of
• pathological of
  • gross pathological anatomical entity➞pathological of
• subclass of
  • anatomical entity➞subclass of
    • constructed cell type➞subclass of
    • evolved anatomical entity➞subclass of
      • cellular evolved anatomical entity➞subclass of
      • evolved cell type➞subclass of
        • species neutral evolved cell type➞subclass of
        • species specific evolved cell type➞subclass of
      • gross evolved anatomical entity➞subclass of
        • species neutral gross evolved anatomical entity➞subclass of
        • species specific gross evolved anatomical entity➞subclass of
    • gross constructed anatomical entity➞subclass of
    • gross pathological anatomical entity➞subclass of
    • pathological cell type➞subclass of
  • atomic phenotypic feature➞subclass of
  • atomic trait➞subclass of

Types

Built in

• Bool
• ElementIdentifier
• NCName
• NodeIdentifier
• URI
• URIorCURIE
• XSDDate
• XSDDateTime
• XSDTime
• float
• int
• str

Defined

• Boolean (Bool) - A binary (true or false) value
• Date (XSDDate) - a date (year, month and day) in an idealized calendar
• Datetime (XSDDateTime) - The combination of a date and time
• Double (float) - A real number that conforms to the xsd:double specification
• Float (float) - A real number that conforms to the xsd:float specification
• Integer (int) - An integer
• Ncname (NCName) - Prefix part of CURIE
• Nodeidentifier (NodeIdentifier) - A URI, CURIE or BNODE that represents a node in a model.
• Objectidentifier (ElementIdentifier) - A URI or CURIE that represents an object in the model.
• String (str) - A character string
• Time (XSDTime) - A time object represents a (local) time of day, independent of any particular day
• Uri (URI) - a complete URI
• Uriorcurie (URIorCURIE) - a URI or a CURIE

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