Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology.
Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology.
复制标题
DOI：
10.1186/2041-1480-5-34
复制
发表时间：
2014
影响因子：
1.9
通讯作者：
Haendel MA
中科院分区：
文献类型：
--
作者：
Dahdul WM;Cui H;Mabee PM;Mungall CJ;Osumi-Sutherland D;Walls RL;Haendel MA
空间术语在解剖学中用于表示生物体中结构的精确相对位置。虽然这些术语通常在生物学的特定领域内标准化，但它们在不同的分类群中可能会有很大的差异。这种用法上的差异可能会削弱我们在比较不同物种的解剖结构或表型时明确提及解剖位置的能力。我们开发了生物空间本体（BSPO），以标准化描述的空间和拓扑关系的分类群，使可比表型的发现。BSPO目前包含146个类和58个关系，代表解剖轴、梯度、区域、平面、侧面和表面。这些概念可用于多种生物尺度和多种分类群，包括植物、动物和真菌。BSPO用于提供解剖位置描述符的源，用于在解剖本体中逻辑地定义解剖实体类。通过将诸如dorsal_to的空间关系集成到类描述中（例如，“背外侧基板”背侧到一些“上鳃基板”）。BSPO目前用于需要标准化解剖描述符的项目，用于跨多种分类群的表型注释和本体集成。解剖位置类也可用于描述表型差异，如物种内和物种间进化导致的结构位置的形态变化。
Spatial terminology is used in anatomy to indicate precise, relative positions of structures in an organism. While these terms are often standardized within specific fields of biology, they can differ dramatically across taxa. Such differences in usage can impair our ability to unambiguously refer to anatomical position when comparing anatomy or phenotypes across species. We developed the Biological Spatial Ontology (BSPO) to standardize the description of spatial and topological relationships across taxa to enable the discovery of comparable phenotypes. BSPO currently contains 146 classes and 58 relations representing anatomical axes, gradients, regions, planes, sides, and surfaces. These concepts can be used at multiple biological scales and in a diversity of taxa, including plants, animals and fungi. The BSPO is used to provide a source of anatomical location descriptors for logically defining anatomical entity classes in anatomy ontologies. Spatial reasoning is further enhanced in anatomy ontologies by integrating spatial relations such as dorsal_to into class descriptions (e.g., ‘dorsolateral placode’ dorsal_to some ‘epibranchial placode’). The BSPO is currently used by projects that require standardized anatomical descriptors for phenotype annotation and ontology integration across a diversity of taxa. Anatomical location classes are also useful for describing phenotypic differences, such as morphological variation in position of structures resulting from evolution within and across species.
登录
查看更多内容
影响因子：
4.9
作者：
Cooper L;Walls RL;Elser J;Gandolfo MA;Stevenson DW;Smith B;Preece J;Athreya B;Mungall CJ;Rensing S;Hiss M;Lang D;Reski R;Berardini TZ;Li D;Huala E;Schaeffer M;Menda N;Arnaud E;Shrestha R;Yamazaki Y;Jaiswal P
通讯作者：
Jaiswal P
影响因子：
3
作者：
Deegan (nee Clark), Jennifer I.;Dimmer, Emily C.;Mungall, Christopher J.
通讯作者：
Mungall, Christopher J.
脊椎动物骨骼系统的统一解剖本体。
影响因子：
3.7
作者：
Dahdul WM;Balhoff JP;Blackburn DC;Diehl AD;Haendel MA;Hall BK;Lapp H;Lundberg JG;Mungall CJ;Ringwald M;Segerdell E;Van Slyke CE;Vickaryous MK;Westerfield M;Mabee PM
通讯作者：
Mabee PM
影响因子：
3.7
作者：
Dahdul WM;Balhoff JP;Engeman J;Grande T;Hilton EJ;Kothari C;Lapp H;Lundberg JG;Midford PE;Vision TJ;Westerfield M;Mabee PM
通讯作者：
Mabee PM
影响因子：
56.9
作者：
Finnerty, JR;Pang, K;Martindale, MQ
通讯作者：
Martindale, MQ