BiomatArtifactObjectBranchFoundation
Foundational semantic framework for material objects (biomaterial and instrument branches)
Initial efforts to organize the root of the material branches (Biomaterial and Instrument) led to the creation of a base class artifact_object intended as a means of separating biologically-based objects (immortal_cell, ChEBI_object, xenograft, etc.) from non-biological physical materials artificially shaped through human craft (e.g., Instruments, Cardinal_part_of_instrument, etc.).
Further review by the larger group of OBI developers that took place during the bi-annual OBI Developer meeting in July 2007 at the NIH in Bethesda, MD led to two fundamental questions:
- It appears quite difficult to consistently define the boundary between biological and artificial materials. The existence of classes under Biomaterial such as ExperimentalBiomaterialEntity and NaturalBiomaterialEntity seem to highten as opposed to resolve the issue by drawing attention to the arbitrary and potentially inconsistent boundary between natural and artificial biologically-derived material.
- Whether or not the boundary is considered arbitrary, the question remains as to what the primary classification for material objects should be. The discussion has focussed on:
- whether and/or how to use the ontology normalization Design Pattern to define the core hierarchy with alternative hierarchies defined via inference?
- if normalization is to be used, how and which ObjectProperties and Qualities will be required to support inferring all the needed classification hierarchies?
- if normalization is to be used, will we want to deploy a version of OBI where inferred classification hierarchies are saved as asserted classes for the convenience of the community of OBI users?
comment from HP, yes I think we need the convenient version
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Contents |
Discussion Participants
- Bill Bug (BB)
- Cristian Cocos (CC)
- Gilberto Fragoso (GF)
- Frank Gibson (FG)
- Allyson Lister (AL)
- Chris Mungall (CM)
- Helen Parkinson (HP)
- Bjoern Peters (BP)
- Matthew Pocock (MP)
- Philippe Rocca-Serra (PR)
- Daniel Schober (DS)
- Alan Ruttenberg (AR)
Developer Discussions
- Core Material Object Classification
- Current (2007-07-19) High-level OBI subclasses of bfo:Object
- Proposed Object Hierarchy
- Separating Objects and ObjectAggregates
- Use of OBI Relations and/or OBO Relations
- Contribution from other branches in defining complex classifications of material objects
- Use of PATO:Qualities
- Use of OBI:Role
- Use of OBI:Function
