Aitken Stuart
School of Informatics, The University of Edinburgh, Edinburgh EH8 9LE, United Kingdom.
Bioinformatics. 2005 Jun 1;21(11):2773-9. doi: 10.1093/bioinformatics/bti409. Epub 2005 Mar 29.
Anatomy ontologies have a growing role in bioinformatics-for example, in indexing gene expression data in model organisms. To relate or draw conclusions from data so indexed, anatomy ontologies must be equipped with the formal vocabulary that would allow statements about meronomy to be qualified by constraints such as part of the male or part at the embryonic stage. Lacking such a vocabulary, anatomists have built this information into the structure of the ontology or into anatomical terms. For example, in the FlyBase anatomy for drosophila, the term larval abdominal segment encodes the stage in the term, while the terms male genital disc and female genital disc encode the sex. It remains implicit that a fly has one and only one of these parts during its larval stage. Such indicators of context can and should be represented explicitly in the ontology.
The framework we have defined for anatomical ontologies allows the canonical anatomy structures of a given species to be those common to all sexes, and to have either male, female or hermaphrodite parts--but not combinations of the latter. Temporal aspects of development are addressed by associating a stage with organism parts and requiring a connected anatomy to have parts that exist at a common stage. Both sex and anatomical stage are represented by attributes. This formalization clarifies ontological structure and meaning and increases the capacity for formal reasoning about anatomy. The framework also supports generalizations such as vertebrate and invertebrate, thereby allowing the representation of anatomical structures that are common across a sub-phylum.
解剖学本体在生物信息学中的作用日益增强，例如在对模式生物中的基因表达数据进行索引时。为了关联或从如此索引的数据中得出结论，解剖学本体必须配备形式化词汇，以便关于整体-部分关系的陈述能够通过诸如雄性部分或胚胎阶段部分等约束进行限定。由于缺乏这样的词汇，解剖学家已将此信息构建到本体结构或解剖学术语中。例如，在果蝇的FlyBase解剖学中，术语“幼虫腹部节段”在术语中编码了阶段，而术语“雄性生殖盘”和“雌性生殖盘”编码了性别。不言而喻的是，果蝇在其幼虫阶段有且仅有这些部分中的一个。这种上下文指标能够且应该在本体中明确表示。
我们为解剖学本体定义的框架允许给定物种的典型解剖结构为所有性别共有的结构，并具有雄性、雌性或雌雄同体部分，但不是后两者的组合。发育的时间方面通过将一个阶段与生物体部分相关联并要求一个相连的解剖结构具有在共同阶段存在的部分来解决。性别和解剖阶段均由属性表示。这种形式化澄清了本体结构和含义，并增加了对解剖学进行形式化推理的能力。该框架还支持诸如脊椎动物和无脊椎动物等概括，从而允许表示跨亚门共有的解剖结构。
