CLO: The cell line ontology.
CLO: The cell line ontology.
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DOI：
10.1186/2041-1480-5-37
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发表时间：
2014
影响因子：
1.9
通讯作者：
He Y
中科院分区：
文献类型：
--
作者：
Sarntivijai S;Lin Y;Xiang Z;Meehan TF;Diehl AD;Vempati UD;Schürer SC;Pang C;Malone J;Parkinson H;Liu Y;Takatsuki T;Saijo K;Masuya H;Nakamura Y;Brush MH;Haendel MA;Zheng J;Stoeckert CJ;Peters B;Mungall CJ;Carey TE;States DJ;Athey BD;He Y
细胞系在生物医学研究中有着广泛的应用。基于社区的细胞系本体（Cell Line Ontology， CLO）是覆盖细胞系领域的OBO Foundry库的成员。自两年前出版以来，已经进行了重大更新，包括加入CLO联盟的新组，新的细胞系细胞，与细胞本体（CL）和生物医学研究本体的上层对齐，以及逻辑扩展。CLO、CL和OBI之间的合作已经建立了细胞系特定术语的共识定义，如“细胞系”、“细胞系细胞”、“细胞系培养”以及“致命”与“不朽”细胞系细胞。细胞系是一种基因稳定的培养细胞群，其中包含单个细胞系细胞。CLO的层次结构是基于CL中定义的体内细胞类型和UBERON跨物种解剖本体中定义的组织类型（细胞系细胞来源于组织类型）的层次结构构建的。新的层次结构使浏览、查询和执行自动分类变得更加容易。我们最近从RIKEN BRC细胞库向CLO添加了代表2000多个细胞系细胞的类。总的来说，CLO现在包含约38,000类特定的细胞系细胞，这些细胞来自于来自各种生物体的200多种体内细胞类型。CLO已应用于不同的生物医学研究。示例案例研究包括注释和分析EBI ArrayExpress数据、生物测定和宿主-疫苗/病原体相互作用。CLO的用途超出了细胞系类型的目录。CLO与相关本体论的结合以及本体论推理器的使用将支持复杂的推理，以推进翻译信息学的发展。
Cell lines have been widely used in biomedical research. The community-based Cell Line Ontology (CLO) is a member of the OBO Foundry library that covers the domain of cell lines. Since its publication two years ago, significant updates have been made, including new groups joining the CLO consortium, new cell line cells, upper level alignment with the Cell Ontology (CL) and the Ontology for Biomedical Investigation, and logical extensions. Collaboration among the CLO, CL, and OBI has established consensus definitions of cell line-specific terms such as ‘cell line’, ‘cell line cell’, ‘cell line culturing’, and ‘mortal’ vs. ‘immortal cell line cell’. A cell line is a genetically stable cultured cell population that contains individual cell line cells. The hierarchical structure of the CLO is built based on the hierarchy of the in vivo cell types defined in CL and tissue types (from which cell line cells are derived) defined in the UBERON cross-species anatomy ontology. The new hierarchical structure makes it easier to browse, query, and perform automated classification. We have recently added classes representing more than 2,000 cell line cells from the RIKEN BRC Cell Bank to CLO. Overall, the CLO now contains ~38,000 classes of specific cell line cells derived from over 200 in vivo cell types from various organisms. The CLO has been applied to different biomedical research studies. Example case studies include annotation and analysis of EBI ArrayExpress data, bioassays, and host-vaccine/pathogen interaction. CLO’s utility goes beyond a catalogue of cell line types. The alignment of the CLO with related ontologies combined with the use of ontological reasoners will support sophisticated inferencing to advance translational informatics development.
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影响因子：
64.8
作者：
Mueller, Franz-Josef;Laurent, Louise C.;Kostka, Dennis;Ulitsky, Igor;Williams, Roy;Lu, Christina;Park, In-Hyun;Rao, Mahendra S.;Shamir, Ron;Schwartz, Philip H.;Schmidt, Nils O.;Loring, Jeanne F.
通讯作者：
Loring, Jeanne F.
影响因子：
3.7
作者：
Ganzinger, Matthias;He, Shan;Knaup, Petra
通讯作者：
Knaup, Petra
影响因子：
3.7
作者：
Chen F;He Y
通讯作者：
He Y
影响因子：
14.9
作者：
Masuya H;Makita Y;Kobayashi N;Nishikata K;Yoshida Y;Mochizuki Y;Doi K;Takatsuki T;Waki K;Tanaka N;Ishii M;Matsushima A;Takahashi S;Hijikata A;Kozaki K;Furuichi T;Kawaji H;Wakana S;Nakamura Y;Yoshiki A;Murata T;Fukami-Kobayashi K;Mohan S;Ohara O;Hayashizaki Y;Mizoguchi R;Obata Y;Toyoda T
通讯作者：
Toyoda T
影响因子：
46.9
作者：
Smith, Barry;Ashburner, Michael;Lewis, Suzanna
通讯作者：
Lewis, Suzanna