Top 10 Errors to Avoid When Building an Ontology

Provided at the request of participants in the First OBO Foundry Summit

 

  1. Mixing singulars and plurals:
    "National Socialism is_a political systems"
    -- MeSH
  2. Mixing concepts with entities in reality:
    "CONCEPT is_a Veterinary proprietary drug AND/OR biological"
    -- SNOMED CT
  3. Mixing words with entities in reality:
    distinguishing 26 kinds of chemicals:
    "chemicals whose names begin with A",
    "chemicals whose names begin with B"
    -- Read Codes
  4. Mixing ontology and epistemology:
    "'no known allergies' is an allergy to the allergen 'no known allergies'" -- Cerner
    "cardiac output is_a Laboratory or Test Result or Diagnostic Procedure"
    -- UMLS Semantic Network
  5. Confusing entities with data:
    "contact area of molecule has type integer"
    "interacting atom pairs has type string"
    -- early versions of Immune Epitope Ontology
  6. Using 'other':
    "Other problems with special functions";
    "Other motorvehicle non-traffic accident of other and unspecified nature injuring passenger in motor vehicle other than motorcycle"
    -- early versions of Disease Ontology (DO)
  7. Classifying entities on the basis of incidental features:
    "classification of humans by bra cup size" -- CYC
    "Cell is_a Plant Cell" -- old versions of Plant Ontology
    "Water is a type of Nursing Phenomenon of Physical Environment with the specific characteristics:
    Clear liquid compound of hydrogen and oxygen that is essential for most plant and animal life influencing life and development of human beings."
    -- International Classification of Nursing Procedures
  8. Using circular definitions:
    "An integer_number is an arithmetic_number that is an integer number"
    -- ISO 15926 Oil and Gas Ontology
  9. Overloading is_a:
    "virus is_a environment ontology" -- Gramene Environment Ontology
    "cow is_a kingdom animalia"; "Prisheksninsk pig breed is_a
    organism"
    -- SNOMED CT
  10. Not Thinking!
    "vomitus contains carrot" -- GALEN
    "repair and maintenance of wheelchair is_a disease" -- early versions of DO
    "menopause part_of death" -- early versions of GO

 

More details and more examples of types of errors can be found in:
http://ontology.buffalo.edu/smith/ppt/Gene%20Ontology/STOP_GO_5_04.ppt
http://ontology.buffalo.edu/smith/ppt/Gene%20Ontology/nci_feb_2004.ppt
http://www.ifomis.org/bfo/manual

See a streaming video lecture course on positive ontology methodology.
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