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.

Further Reading:

• The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration, Nature Biotechnology 25 (2007), 1251-1255.
• Mistakes in medical ontologies: where do they come from and how can they be detected? Ceusters, W., Smith, B., Kumar, A. & Dhaen, C. Stud. Health Technol. Inform. 102, 145–164 (2004).
• A terminological and ontological analysis of the NCI Thesaurus. Ceusters, W., Smith, B. & Goldberg, L. Methods Inf. Med. 44, 498–507 (2005).
• Relations in biomedical ontologies. Smith, B. et al. Genome Biol. [online] 6, R46 (2005).