Basic Formal Ontology Barry Smith August 26, 2013

Continuant Occurrent Independent Continuant Dependent Continuant Basic Formal Ontology 2

Anatomy Ontology (FMA*, CARO) Environment Ontology (EnvO) Infectious Disease Ontology (IDO*) Biological Process Ontology (GO*) Cell Ontology (CL) Cellular Component Ontology (FMA*, GO*) Phenotypic Quality Ontology (PaTO) Subcellular Anatomy Ontology (SAO) Sequence Ontology (SO*) Molecular Function (GO*) Protein Ontology (PRO*) Extension Strategy + Modular Organization top level mid-level domain level Information Artifact Ontology (IAO) Ontology for Biomedical Investigations (OBI) Spatial Ontology (BSPO) Basic Formal Ontology (BFO) 3/24

continuant independent continuant portion of material object fiat object part object aggregate object boundary site dependent continuant generically dependent continuant information artifact specifically dependent continuant quality realizable entity function role disposition spatial region 0D-region 1D-region 2D-region 3D-region BFO 1.1:continuant

occurrent processual entity process fiat process part process aggregate process boundary processual context spatiotemporal region scattered spatiotemporal region connected spatiotemporal region spatiotemporal instant spatiotemporal interval temporal region scattered temporal region connected temporal region temporal instant temporal interval BFO1.1:occurrent

More than 100 Ontology projects using BFO

Users of BFO Ontology for Risks Against Patient Safety (RAPS/REMINE) eagle-i an VIVO (NCRR) Emotion Ontology Financial Report Ontology (SEC XBRL) IDO Infectious Disease Ontology (NIAID) US Army Biometrics Ontology Sleep Domain Ontology Subcellular Anatomy Ontology (SAO) Translational Medicine Ontology (TMO) Vaccine Ontology (VO) Yeast Ontology (yOWL) Zebrafish Anatomical Ontology (ZAO) 7

Basic Formal Ontology Continuant Occurrent process, event Independent Continuant thing Dependent Continuant quality types instances

Blinding Flash of the Obvious Continuant Occurrent process, event Independent Continuant thing Dependent Continuant quality quality depends on bearer

Blinding Flash of the Obvious Continuant Occurrent process, event Independent Continuant thing Dependent Continuant quality, … event depends on participant

Roles pertain not to what a thing enduringly is, but to the part it plays, e.g. in some operation Continuant Occurrent process, event Independent Continuant thing Dependent Continuant role process is change in quality

General lessons for ontology success incorporated into BFO Common traffic laws for building and using ontologies Lessons learned and disseminated as common guidelines – all developers are doing it the same way Ontologies built by domain experts

Universality (low hanging fruit) Start with simple assertions which you know to be universally true hand part_of body cell death is_a death pneumococcal bacterium is_a bacterium (Computers need to be led by the hand)

Basic Formal Ontology (Top Level) Continuant Occurrent Independent Continuant Dependent Continuant Anatomical Structure Process Stage Quality 14

OBO Foundry organized in terms of Basic Formal Ontology through the methodology of downward population Each Foundry ontology can be seen as an extension of a single upper level ontology (BFO) 15

Continuant Independent Continuant Dependent Continuant QualityDisposition 16

depends_on Continuant Occurrent process, event Independent Continuant thing Dependent Continuant quality temperature depends on bearer 17

this particular case of redness (of a particular fly eye) the universal red instantiates an instance of eye (in a particular fly) the universal eye instantiates depends_on 18 Phenotype Ontology (PATO)

the particular case of redness (of a particular fly eye) red instantiates an instance of an eye (in a particular fly) eye instantiates depends on coloranatomical structure is_a 19

Experience with BFO in building ontologies provides a community of skilled ontology developers and users associated logical tools documentation for different types of users a methodology for building conformant ontologies by starting with BFO and populating downwards

Conclusion Ontologists have established best practices –for building ontologies –for linking ontologies –for evaluating ontologies –for applying ontologies which have been thoroughly tested in use and which conform precisely to the extension strategy from a single upper level