Jansen Ludger, Schulz Stefan
Institute of Philosophy, University of Rostock, 18051 Rostock, Germany.
J Biomed Semantics. 2011 Aug 9;2 Suppl 4(Suppl 4):S2. doi: 10.1186/2041-1480-2-S4-S2.
In biomedical ontologies, mereological relations have always been subject to special interest due to their high relevance in structural descriptions of anatomical entities, cells, and biomolecules. This paper investigates two important subrelations of has_proper_part, viz. the relation has_grain, which relates a collective entity to its multiply occurring uniform parts (e.g., water molecules in a portion of water), and the relation has_component, which relates a compound to its constituents (e.g., molecules to the atoms they consist of).
We distinguish between four kinds of complex entities and characterize them in first order logic. We then discuss whether similar characterizations could be given in description logics, and finally apply the results to mixtures.
At first sight, collectives and compounds seem to be disjoint categories. Their disjointness, however, relies on agreement about what are uniform entities, and thus on the granularity of description. For instance, the distinction between isomeric subtypes of a molecule can be important in one use case but might be neglected in another one. We demonstrate that, as implemented in the BioTop domain upper level ontology, equivalence or subsumption between different descriptions of same or similar entities cannot be achieved. Using OWL-DL, we propose a new design pattern that avoids primitive subrelations at the expense of more complex descriptions and thus supports the needed inferences.
在生物医学本体论中，由于分体关系在解剖实体、细胞和生物分子的结构描述中具有高度相关性，因此一直备受关注。本文研究了“有真部分”（has_proper_part）的两个重要子关系，即“有颗粒”（has_grain）关系，它将一个集合实体与其多个出现的均匀部分相关联（例如，一部分水中的水分子），以及“有成分”（has_component）关系，它将一个化合物与其组成部分相关联（例如，分子与其所由的原子）。
我们区分了四种复杂实体并用一阶逻辑对其进行了刻画。然后我们讨论了在描述逻辑中是否可以给出类似的刻画，最后将结果应用于混合物。
乍一看，集合体和化合物似乎是不相交的类别。然而，它们的不相交依赖于关于什么是均匀实体的一致意见，因此依赖于描述的粒度。例如，分子的同分异构亚型之间的区别在一个用例中可能很重要，但在另一个用例中可能会被忽略。我们证明，如在BioTop领域上层本体中所实现的，对于相同或相似实体的不同描述之间无法实现等价或包含关系。使用OWL-DL，我们提出了一种新的设计模式，该模式以更复杂的描述为代价避免了原始子关系，从而支持所需的推理。
