http://icbo.buffalo.edu/2011/slides

BFO 2.0 Proposal

Barry Smith7/28/2011

BFO 2 Editors’ VersionBFO 2 OWL

The basic idea:• BFO 2 Editors’ Version will guide

implementations and further development• Working with BFO 2 OWL will ensure

consistency with BFO 2 Editors’ Version

BFO 2 OWL

End August: new release of BFO in OWL 2 DL– new URIs conformant with OBO Foundry– relations included with domains and ranges (see

below)– defining relation expressions needed for OBO

Foundry use• e.g. has_plasma_membrane_part

a linguistic shortcut (macro) for talking about parts of plasma membrances

Region Terms

1. We will document a strategy for using BFO region terms, requiring in each case the specification of a frame of reference.

Top level relations incorporated into BFO

We will incorporate into BFO the upper-level relations in RO needed to make BFO relationally self-contained. We will document a procedure whereby new relation expressions (shortcuts) can be defined using the relation-resources in BFO 2. We will create a repository where they can be curated and made available for re-use by others (to ensure interoperability).

Issues

For example:a quality_of b = a inheres_in b and a is_a quality

Users are encouraged to submit their own relational shortcuts in this way, to create

Spatial Extensions, Temporal Extensions …

Numerical values and assertions about processes

We will document a strategy for annotating or regimenting data involving numerical values and assertions about processes.

***Intuition: if you have 3 apples in a box, you do not have 4 first-class entities: the 3 apples, plus the number 3.Analogously: if you have a process that is a 3bpm-process, then you do not have 2 first-class entities: the process, plus the 3bpm.

quality: John’s blood glucose level

participates_inOBI process:

this specific assay

inheres_in

John

deviceparticipates_in

part_of screen

has_specified_output

quality: ‘120 mg/dL’-shaped

pattern

IAO:measurement datum

is_about concretized_by

inheres_inportion of blood

derived_from

Numerical Value Example

process: John’s heart beating

has_participantOBI process:

this specific assay

has_participant

John

device

has_participant

has_part screen

has_specified_output quality: ‘120

mg/dL’-shaped pattern

IAO:measurement datum

is_about concretized_by

inheres_in

Process Predication Example

Device or human ear …

is in each case a reliable means of arriving at information of the relevant sortThis means: • 1. it has been built according to an evolutionary

stable or specified process • 2. it matches the other instances of the same type

produced as outputs of this process• 3. the information produced as output by other

instances of this type has been positively tested for accuracy