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

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.

Issues 1.We will document a strategy for using BFO region terms, requiring in each case the specification of a suitable frame of reference – region terms are needed e.g. to annotate data resting on assignments of spatiotemporal coordinates to observed phenomena – some view regions as information artifacts, some view regions as first-order entities; BFO 2.0 should be interpretable as consistent with both views

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_in OBI process: this specific assay inheres_in John device participates_in part_of screen has_specified _output quality: ‘120 mg/dL’-shaped pattern IAO:measurement datum is_about concretized_by inheres_in portion of blood derived_from Numerical Value Example

process: John’s heart beating has_participant OBI 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 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