A unified anatomy ontology of the vertebrate skeletal system.
A unified anatomy ontology of the vertebrate skeletal system.
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脊椎动物骨骼系统的统一解剖本体。
DOI：
10.1371/journal.pone.0051070
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Mabee PM
中科院分区：
文献类型：
--
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
骨骼在比较脊椎动物形态学、古生物学、生物力学、发育生物学和系统学研究中具有根本重要性。受需要对脊椎动物不同骨骼表型进行计算访问和比较推理的研究问题的推动，我们开发了骨骼系统解剖概念模块，即脊椎动物骨骼解剖本体（VSAO），以适应和统一特定物种（小鼠、青蛙爪蟾、斑马鱼）和多物种（硬骨鱼、两栖动物）脊椎动物解剖学本体。以前这些术语之间的差异甚至阻止了与脊椎动物形态相关的数据库之间的简单查询。该高级和特定骨骼术语模块目前包括 223 个定义术语和 179 个同义词，整合了骨骼细胞、组织、生物过程、器官（骨骼和软骨等骨骼元素）以及骨骼系统的细分。 VSAO 旨在与其他本体集成，包括通用解剖学参考本体 (CARO)、基因本体 (GO)、Uberon 和细胞本体 (CL)，并且它可以免费提供给社区，以便使用研究所需的附加术语进行更新。其结构适应脊椎动物物种在发育、结构和组成方面的解剖学差异。用这种本体论对不同脊椎动物表型进行注释将使对表型多样性的全谱进行新颖的探究成为可能。
The skeleton is of fundamental importance in research in comparative vertebrate morphology, paleontology, biomechanics, developmental biology, and systematics. Motivated by research questions that require computational access to and comparative reasoning across the diverse skeletal phenotypes of vertebrates, we developed a module of anatomical concepts for the skeletal system, the Vertebrate Skeletal Anatomy Ontology (VSAO), to accommodate and unify the existing skeletal terminologies for the species-specific (mouse, the frog Xenopus, zebrafish) and multispecies (teleost, amphibian) vertebrate anatomy ontologies. Previous differences between these terminologies prevented even simple queries across databases pertaining to vertebrate morphology. This module of upper-level and specific skeletal terms currently includes 223 defined terms and 179 synonyms that integrate skeletal cells, tissues, biological processes, organs (skeletal elements such as bones and cartilages), and subdivisions of the skeletal system. The VSAO is designed to integrate with other ontologies, including the Common Anatomy Reference Ontology (CARO), Gene Ontology (GO), Uberon, and Cell Ontology (CL), and it is freely available to the community to be updated with additional terms required for research. Its structure accommodates anatomical variation among vertebrate species in development, structure, and composition. Annotation of diverse vertebrate phenotypes with this ontology will enable novel inquiries across the full spectrum of phenotypic diversity.
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DOI：
10.1093/bioinformatics/bts048
发表时间：
2012-04-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Niknejad A;Comte A;Parmentier G;Roux J;Bastian FB;Robinson-Rechavi M
通讯作者：
Robinson-Rechavi M
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：
12.3
作者：
Mungall CJ;Gkoutos GV;Smith CL;Haendel MA;Lewis SE;Ashburner M
通讯作者：
Ashburner M
影响因子：
14.9
作者：
Bradford Y;Conlin T;Dunn N;Fashena D;Frazer K;Howe DG;Knight J;Mani P;Martin R;Moxon SA;Paddock H;Pich C;Ramachandran S;Ruef BJ;Ruzicka L;Bauer Schaper H;Schaper K;Shao X;Singer A;Sprague J;Sprunger B;Van Slyke C;Westerfield M
通讯作者：
Westerfield M
影响因子：
12.3
作者：
Mungall CJ;Torniai C;Gkoutos GV;Lewis SE;Haendel MA
通讯作者：
Haendel MA