构建秀丽隐杆线虫的细胞与解剖本体论。
Building a cell and anatomy ontology of Caenorhabditis elegans.
作者信息
Lee Raymond Y N, Sternberg Paul W
机构信息
WormBase, California Institute of Technology, Pasadena, CA 91125, USA.
出版信息
Comp Funct Genomics. 2003;4(1):121-6. doi: 10.1002/cfg.248.
Abstract
We are endowed with a rich knowledge about Caenorhabditis elegans. Its stereotyped anatomy and development has stimulated research and resulted in the accumulation of cell-based information concerning gene expression, and the role of specific cells in developmental signalling and behavioural circuits. To make the information more accessible to sophisticated queries and automated retrieval systems, WormBase has begun to construct a C. elegans cell and anatomy ontology. Here we present our strategies and progress.
摘要
我们对秀丽隐杆线虫拥有丰富的知识。其固定的解剖结构和发育过程激发了研究，并积累了有关基因表达的基于细胞的信息，以及特定细胞在发育信号传导和行为回路中的作用。为了使这些信息更便于复杂查询和自动检索系统使用，WormBase已开始构建秀丽隐杆线虫细胞与解剖本体。在此，我们展示我们的策略和进展。
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本文引用的文献
1
Predictive value of compression ultrasonography for deep vein thrombosis in symptomatic outpatients: clinical implications of the site of vein noncompressibility.症状性门诊患者中超声压迫检查对深静脉血栓形成的预测价值：静脉不可压缩部位的临床意义。
Arch Intern Med. 2000 Feb 14;160(3):309-13. doi: 10.1001/archinte.160.3.309.
2
Formation of the vulva in Caenorhabditis elegans: a paradigm for organogenesis.秀丽隐杆线虫外阴的形成：器官发生的范例
Development. 1999 Feb;126(4):691-9. doi: 10.1242/dev.126.4.691.
3
Morphogenesis of the C. elegans hermaphrodite uterus.秀丽隐杆线虫雌雄同体子宫的形态发生。
Development. 1996 Nov;122(11):3617-26. doi: 10.1242/dev.122.11.3617.
4
Symmetry breakage in the development of one-armed gonads in nematodes.线虫单臂性腺发育中的对称性破坏。
Development. 1996 Jul;122(7):2129-42. doi: 10.1242/dev.122.7.2129.
5
Evolution of cell lineage and pattern formation in the vulval equivalence group of rhabditid nematodes.小杆线虫外阴等价组中细胞谱系的演化与模式形成
Dev Biol. 1995 Jan;167(1):61-74. doi: 10.1006/dbio.1995.1007.
6
The Caenorhabditis elegans male: postembryonic development of nongonadal structures.秀丽隐杆线虫雄性：非性腺结构的胚后发育
Dev Biol. 1980 Aug;78(2):542-76. doi: 10.1016/0012-1606(80)90352-8.
7
Gonadal cell lineages of the nematode Panagrellus redivivus and implications for evolution by the modification of cell lineage.线虫类小杆线虫的性腺细胞谱系及其通过细胞谱系修饰对进化的影响
Dev Biol. 1981 Nov;88(1):147-66. doi: 10.1016/0012-1606(81)90226-8.
8
The embryonic cell lineage of the nematode Caenorhabditis elegans.秀丽隐杆线虫的胚胎细胞谱系。
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9
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J Comp Neurol. 1975 Apr 1;160(3):313-37. doi: 10.1002/cne.901600305.
10
Post-embryonic cell lineages of the nematode, Caenorhabditis elegans.线虫秀丽隐杆线虫的胚胎后细胞谱系。
Dev Biol. 1977 Mar;56(1):110-56. doi: 10.1016/0012-1606(77)90158-0.
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