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http://icbo.buffalo.edu/2011/slides. BFO 2.0 Proposal. Barry Smith 7/28/2011. BFO 2 Editors ’ Version BFO 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.

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Http icbo buffalo edu 2011 slides

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


Bfo 2 0 proposal

BFO 2.0 Proposal

Barry Smith

7/28/2011


Bfo 2 editors version bfo 2 owl

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

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

Region Terms

  • 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

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

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

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.


Icbo buffalo 2011 slides

IAO:measurement datum

is_about

concretized_by

quality: John’s blood glucose level

has_specified

_output

quality: ‘120 mg/dL’-shaped pattern

inheres_in

OBI process:

this specific assay

portion of blood

participates_in

inheres_in

derived_from

participates_in

device

screen

part_of

John

Numerical Value Example


Icbo buffalo 2011 slides

IAO:measurement datum

is_about

concretized_by

process: John’s heart beating

has_specified

_output

quality: ‘120 mg/dL’-shaped pattern

has_participant

OBI process:

this specific assay

has_participant

inheres_in

device

screen

has_part

has_participant

Process Predication Example

John


Device or human ear

Device or human ear …

is in each case a reliable means of arriving at information of the relevant sort

This 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


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