http://icbo.buffalo.edu/2011/slides. bfo 2.0 proposal barry smith 7/28/2011
TRANSCRIPT
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