1. How BFO Deals with Data from Multiple Contexts
Barry Smith
2018 Ontology Summit
February 8, 2018

2. 1. Origins of BFO 2. Environment Ontology 3. Environments as Systems
Geospatial Ontology
Theory of Granular Partitions
Open Biomedical Ontologies Foundry
Common Core Ontologies
2. Environment Ontology
3. Environments as Systems

3. RCC (Region Connection Calculus)
disconnected (DC)
externally connected (EC)
equal (EQ)
partially overlapping (PO)
tangential proper part (TPP)
tangential proper part inverse (TPPi)
non-tangential proper part (NTPP)
non-tangential proper part inverse (NTPPi)

4. Example: joint anatomy
joint HAS-HOLE joint space
joint capsule IS-OUTER-LAYER-OF joint
meniscus
IS-INCOMPLETE-FILLER-OF joint space
IS-TOPO-INSIDE joint capsule
IS-NON-TANGENTIAL-MATERIAL-PART-OF joint
joint
IS-CONNECTOR-OF bone X
IS-CONNECTOR-OF bone Y
synovia
synovial membrane IS-BONAFIDE-BOUNDARY-OF joint space

5. objects occupy space – they are located in BFO: spatial regions

6. Universe/Periodic Table
animal
bird
canary
ostrich
fish
Universe/Periodic Table
folk biology
partition of DNA space

7. Universe/Periodic Table
animal
bird
canary
ostrich
fish
Universe/Periodic Table
both are transparent partitions of one and the same reality

8. France
Departments
Regions

9. Perspectivalism
Perspectivalism
Different partitions may represent cuts through the same reality which are skew to each other

10. An organism is a totality of atoms
An organism is a totality of molecules
An organism is a totality of cells
An organism is a single unitary substance
... all of these express veridical partitions

11. Ontology like cartography
must work with maps at different scales and with maps picking out different dimensions of invariants

12. Basic Formal Ontology
map layers

14. EMMO the European Materials Modelling Ontology
Emanuele Ghedini (University of Bologna)
Adham Hashibon (Fraunhofer IWM)
Jesper Friis (SINTEF)
Gerhard Goldbeck (Goldbeck Consulting)
Georg Schmitz (ACCESS)
Anne de Baas (European Commission)

15. BFO Hierarchy
EMMO RELIES ON THE STRUCTURE OF BASIC FORMAL ONTOLOGY (BFO).
The Basic Formal Ontology (BFO) is a small, upper level ontology that is designed for use in supporting information retrieval, analysis and integration in scientific and other domains.
BFO is a genuine upper ontology. Thus it does not contain physical, chemical, biological or other terms which would properly fall within the coverage domains of the special sciences.
The theory behind BFO was developed in first by Barry Smith and Pierre Grenon.
NOTE: material_entity (BFO) is any independent continuant that has some portion of matter as part (e.g. ‘human being’)
Hence: material_entity (BFO) is not the same as ‘material entity’ in RoMM and not the same as ‘material’ from the chemistry or engineering point of view.

16. BFO Hierarchy
EMMO RELIES ON THE STRUCTURE OF BASIC FORMAL ONTOLOGY (BFO).
The Basic Formal Ontology (BFO) is a small, upper level ontology that is designed for use in supporting information retrieval, analysis and integration in scientific and other domains.
BFO is a genuine upper ontology. Thus it does not contain physical, chemical, biological or other terms which would properly fall within the coverage domains of the special sciences.
The theory behind BFO was developed in first by Barry Smith and Pierre Grenon.
NOTE: material_entity (BFO) is any independent continuant that has some portion of matter as part (e.g. ‘human being’)
Hence: material_entity (BFO) is not the same as ‘material entity’ in RoMM and not the same as ‘material’ from the chemistry or engineering point of view.

17. EMMO Material Entity Branch Requirements
A robust, flexible and multi-perspective ontological framework for representing materials 1
Since materials are perceived at different scales, the material entities (BFO) should be sub-categorized to cover all granularity levels, so that the same material can be represented in EMMO as a black box or as a collection of sub-parts.
e.g. a molecule seen as a single rigid body
the same molecule seen as a collection of atoms 2

18. EMMO Mereology EMMO Material Entities are defined by a
hierarchy of parthood relations,
combining the concepts of direct parthood and object
With EMMO we create a representation of the real world granularity of material entities that follows physics and materials science perspectives.
A ‘material’ in the user case can be described univocally by declaring entities under EMMO hierarchy.
The basic idea is that the ‘material’ can be represented at different levels of granularity, depending on perspective.
has_part
has_part p n
has_part
has_part
has_part
has_part
has_part e-

19. BFO is a multi-perspectival ontology
Continuant view
Occurrent view
Bicategorial view
Single-perspective view – molecular, cellular, …
Multi-perspective view – how molecules relate to cells …
Contexts ≈perspectives?

20. Contexts ≈ Environments (biological, social, political …)

21. Viewed topologically, biological environments have the structure of holes

22. environment place site niche habitat setting hole spatial region interior location

23. Places are (in first approximation) holes
Rome, Piazza Navona

24. Places are holes
Inner Gorge, Colorado River, Granite Rapids, looking west from Tonto Trail just west of Salt Creek
http//

25. Florence

28. Four Basic Niche Types (Niche as generalized hole)
1: a womb; an egg; a house (better: the interior thereof)
2: a snail’s shell;
3: the niche of a pasturing cow;
4: the niche around a circling buzzard (fiat boundary)

30. BFO:independent_continuant

31. BFO:object (& its siblings)

32. BFO: material_entity and BFO: site occupy BFO: 3-D spatial region

33. Granularity: From geographic to microbiological
From data on locations (cities, factories, jungles, …) to data on bacterial infections – how the interior of one organism or organism part serves as environment for another organism

34. Sites which serve as hosts for bacterial infection
(interior of) lung blood (bacteremia) erythrocyte - plasmodium inhabits red blood cells hepatocyte – plasmodium infects liver cells macrophage gut and oral mucosa, nasal mucosa, vaginal mucosa kidney bladder portion of epithelial tissue

35. Examples of BFO-based biological ontologies
Bacterial Clinical Infectious Diseases Ontology (BCIDO)
Beta Cell Genomics Application Ontology (BCGO)
Biological Collections Ontology (BCO)
Cell Ontology (CL)
Cell Line Ontology (CLO)
Chemical Entities of Biological Interest (CHEBI)
Common Anatomy Reference Ontology (CARO)
Drug Ontology (DRON)
Emotion Ontology (MFOEM)
Environment Ontology (ENVO)
Gene Ontology (GO)
Human Disease Ontology (HDO)
Infectious Disease Ontology (IDO)
Information Artifact Ontology (IAO)
Mental Disease Ontology (MFOMD)
Mental Functioning Ontology (MFO)
Ontology for Adverse Events (OAE)
Ontology for Biobanking (OBIB)
Ontology of Biological and Clinical Statistics (OBCS)
Ontology for Biomedical Investigations (OBI)
Ontology for General Medical Science (OGMS)
Ontology of Medically Related Social Entities (OMRSE)
Oral Health and Disease Ontology (OHD)
Plant Ontology (PO)
Population and Community Ontology (PCO)
Protein Ontology (PRO)
Relations Ontology (RO)
Vaccine Ontology (VO)

36. Ontology Suites Best practice principles for ontology building

37. Hub and spokes approach

38. ontologies are networked together and developed in coordination with each other terms in spokes ontologies are defined logically using terms from ontologies nearer the hub

39. further examples of BFO-based suites
users
date
hub
Common Core Ontologies (CCO)
US Army / I2WD and ARL, IARPA, JIDO, ONR, AFRL …
2010
BFO
Common Intelligence Community Ontology
DNI, CIA, DIA, …
~2014
USGS National Map
United States Geological Survey
Joint Doctrine Ontologies
US Air Force Research Labs (part of CCO)
2015
Transportation Research Informatics Platform (TRIP) Ontologies
Federal Highway Administration (FHWA)
UNEP Ontology Framework
United Nations Environment Programme
2016
Industrial Ontologies Foundry (IOF)
Ontologies to support digital manufacturing (NIST)

40. Examples of ontology suites
domain
date
IRI
hub
Toronto Virtual Enterprise (TOVE)
enterprise
modeling
1998
Yes
Gramene: Trait and Gene Ontologies for Rice
plant science
2002
Open Biomedical Ontologies (OBO) Library
life sciences
2003
(GO)
Semantic Web for Earth and Environmental Terminology (SWEET)
earth and environmental sciences No
Legal Informatics Ontologies (LRI-Core)
legal informatics
2004
Open Biomedical Ontologies (OBO) Foundry
2005
(BFO)
Marine Metadata Interoperability Project
oceano­graphy
2009

41. ~2005 initial OBO Foundry suite
RELATION
TO TIME
GRANULARITY
CONTINUANT
OCCURRENT
INDEPENDENT
DEPENDENT
ORGAN AND
ORGANISM
Organism
(NCBI
Taxonomy)
Anatomical Entity
(FMA, CARO)
Organ
Function
(FMP, CPRO)
Phenotypic Quality (PaTO)
Biological Process
(GO)
CELL AND CELLULAR COMPONENT
Cell
(CL)
Cellular Component
(FMA, GO)
Cellular Function
MOLECULE
Molecule
(ChEBI, SO,
RnaO, PrO)
Molecular Function
Molecular Process
~2005 initial OBO Foundry suite

42. Organism-Level Process
CONTINUANT
OCCURRENT
INDEPENDENT
DEPENDENT
ORGAN AND
ORGANISM
Organism
(NCBI
Taxonomy)
Anatomical Entity
(FMA, CARO)
Organ
Function
(FMP, CPRO)
Phenotypic Quality (PaTO)
Organism-Level Process
(GO)
CELL AND CELLULAR COMPONENT
Cell
(CL)
Cellular Component
(FMA, GO)
Cellular Function
Cellular Process
MOLECULE
Molecule
(ChEBI, SO,
RNAO, PRO)
Molecular Function
Molecular Process
RELATION TO TIME
GRANULARITY
rationale of OBO Foundry coverage = BFO

43. Environment Ontology (EnvO)
RELATION
TO TIME
GRANULARITY
CONTINUANT
OCCURRENT
INDEPENDENT
DEPENDENT
ORGAN AND
ORGANISM
Organism
(NCBI
Taxonomy)
Anatomical Entity
(FMA, CARO)
Organ
Function
(FMP, CPRO)
Phenotypic Quality (PaTO)
Biological Process
(GO)
CELL AND CELLULAR COMPONENT
Cell
(CL)
Cellular Component
(FMA, GO)
Cellular Function
MOLECULE
Molecule
(ChEBI, SO,
RnaO, PrO)
Molecular Function
Molecular Process
Environment Ontology
Environment Ontology (EnvO)

44. ~ 300 ontologies re-using BFO

45. Another view of contexts
Contexts ≈ systems Lemma: Environments ≈ Systems

46. system environmental system ecosystem biome microbiome

47. BFO
ENVO

48. ENVO Definition system
=def. A material entity consisting of multiple components that are causally integrated
Examples: solar system, digestive system, forest ecosystem, subway system
JZ: what components refer to in the definition? Only material entity or any kinds of independent continuant? If components refer to any kind of independent continuant, shall define system as a subclass of independent continuant rather than material entity?

49. ENVO Definition environmental system
= Def. A system which has the disposition to environ one or more material entities.
a environs b = Def. a includes b (partially or wholly) within its site and a causally influences b
Example: The Union Station lost-and-found system
The system includes, for example, the managers of the repository of found items.

50. ENVO Definition ecosystem system environmental system
Def. an environmental system that environs living organisms
biome
microbiome
JZ: in ENVO: Def: An environmental system which includes both living and non-living components. [database_cross_reference:
= ((environmental system and (has part some cellular organisms))) or (has part some collection of organisms) or (determined by some cellular organisms) or (determined by some collection of organisms) or (determined by some plant anatomical entity) or (determined by some anatomical entity)

51. ENVO Definition
biome
=def. an ecosystem that is determined by an ecological community
determined by = def. A system is determined by an entity if the removal of that entity would cause the collapse of that system
(e.g. removing the corals from a coral reef ecosystem would cause that ecosystem to collapse)
​Systems typically break if you take out their biggest parts.​
JZ: in ENVO: Def: An environmental system which includes both living and non-living components. [database_cross_reference:
= ((environmental system and (has part some cellular organisms))) or (has part some collection of organisms) or (determined by some cellular organisms) or (determined by some collection of organisms) or (determined by some plant anatomical entity) or (determined by some anatomical entity)

52. community = Def. a collection of organisms connected by social or biological relations (biotic interactions).
ecological community = Def. a community of at least two different species living in a particular area. 

53. ENVO-based microbiome definition
system
environmental system
ecosystem
biome
microbiome
Def. a biome determined by an ecological community of microbiota
biome is a system – includes both environment and inhabitants

55. The Environment Ontology
BFO
ENVO
PCO
‘is a’ relations
Introducing determined by
AMM: in addition to the population the habitat is mainly determinated by the environmental conditions. The importance of the living organism will play a major role in the niche

56. Incorporating microbiome
BFO
ENVO
PCO
‘is a’ relations
One way to resolve the microbiota / microbiome issue