Method for identifying relevant groups of genes using gene expression profiles
    1.
    发明申请
    Method for identifying relevant groups of genes using gene expression profiles 审中-公开
    使用基因表达谱鉴定相关基因组的方法

    公开(公告)号:US20050130187A1

    公开(公告)日:2005-06-16

    申请号:US10919284

    申请日:2004-08-17

    CPC分类号: G16B25/00 G16B40/00

    摘要: Provided is a method for identifying relevant groups of genes using gene expression profiles. More particularly, it is provided a method for identifying relevant groups of genes using gene expression profiles, which analyzes the gene expression profiles obtained from microarray experiments to automatically extract seed genes of significance and identifies the relevant groups of genes based on the extracted seed genes, so that effective identification is possible regardless of the number of genes and a blind setting of initial input parameters are not required for users to readily use the method, wherein the method comprises the steps of (a) preprocessing the gene expression profiles; (b) setting the number of gene groups to be desired (k) and a input parameter(s); (c) extracting k seed genes (k=1, 2, 3, . . . ,n) based on the set input parameter(s); (d) identifying relevant groups of genes by means of the extracted seed genes; and (e) evaluating the identified relevant groups of genes.

    摘要翻译: 提供了使用基因表达谱鉴定相关基因组的方法。 更具体地,提供了一种使用基因表达谱鉴定相关基因组的方法,其分析从微阵列实验获得的基因表达谱,以自动提取有意义的种子基因,并基于提取的种子基因鉴定相关基因组, 使得有效的识别是可能的,无论基因的数量如何,并且用户不需要初始输入参数的盲目设置来容易地使用该方法,其中该方法包括以下步骤:(a)预处理基因表达谱; (b)设定所需基因组数(k)和输入参数; (c)基于所设置的输入参数提取k个种子基因(k = 1,2,3,...,n); (d)通过提取的种子基因鉴定相关基因组; 和(e)评估所鉴定的相关基因组。

    Biological relationship event extraction system and method for processing biological information
    3.
    发明申请
    Biological relationship event extraction system and method for processing biological information 审中-公开
    生物关系事件提取系统和处理生物信息的方法

    公开(公告)号:US20060136147A1

    公开(公告)日:2006-06-22

    申请号:US11304030

    申请日:2005-12-15

    IPC分类号: G01N33/48

    CPC分类号: G16B50/00

    摘要: A biological relationship extraction system including a biological named entity substitution unit substituting a biological named entity in a biological document with a predetermined substitution name; a structure analyzing unit parsing the biological named entity in the biological document containing the substituted biological named entity; a relationship analyzing unit analyzing a relationship between biological named entities from the biological literature parsed by the structure analyzing unit and selecting relationship candidates; a relationship determining unit determining whether the relationship candidates delivered from the relationship analyzing unit are biologically meaningful and determining a relationship between biological named entities; and a biological named entity assignment storage unit storing the biological named entity and a substitution name corresponding to the biological named entity and providing a substitution name or a biological named entity.

    摘要翻译: 一种生物关系提取系统,其包括用具有预定取代名称的生物文献中的生物命名实体取代生物命名实体取代单元; 解析包含取代的生物命名实体的生物文件中的生物命名实体的结构分析单元; 关系分析单元,从结构分析单元解析的生物学文献中分析生物命名实体之间的关系,并选择关系候选; 关系确定单元,确定从关系分析单元传递的关系候选是否具有生物学意义,并确定生物命名实体之间的关系; 以及生物命名实体分配存储单元,其存储生物命名实体和与生物命名实体相对应的替代名称,并提供替代名称或生物命名实体。

    Method for conceptualizing protein interaction networks using gene ontology
    4.
    发明申请
    Method for conceptualizing protein interaction networks using gene ontology 审中-公开
    使用基因本体概念化蛋白质相互作用网络的方法

    公开(公告)号:US20050137808A1

    公开(公告)日:2005-06-23

    申请号:US10971872

    申请日:2004-10-22

    申请人: Jae Choi Seon Park

    发明人: Jae Choi Seon Park

    摘要: Provided is a method for conceptualizing protein interaction networks. The method conceptualizes and simplifies complicated and enormous protein interaction networks wherein the method comprises the steps of (a) conceptualizing protein nodes that form the protein interaction network as gene ontology concepts to reconfigure the network; (b) integrating nodes including the same concepts in the reconfigured network into one node to generate the network by means of exact match; and (c) integrating several nodes having similar concepts in the generated network into one node to reconfigure the generated network by means of approximate match.

    摘要翻译: 提供了一种用于概念化蛋白质相互作用网络的方法。 该方法概念化并简化了复杂和巨大的蛋白质相互作用网络,其中该方法包括以下步骤:(a)将构成蛋白质相互作用网络的蛋白质节点概念化为基因本体概念以重新配置网络; (b)将包括相同概念的节点在重新配置的网络中集成到一个节点中,以通过精确匹配来生成网络; 以及(c)将具有类似概念的几个节点集成到一个节点中,以通过近似匹配来重构所生成的网络。

    Method and system of verifying protein-protein interaction using text mining
    5.
    发明申请
    Method and system of verifying protein-protein interaction using text mining 审中-公开
    使用文本挖掘验证蛋白质 - 蛋白质相互作用的方法和系统

    公开(公告)号:US20070134756A1

    公开(公告)日:2007-06-14

    申请号:US11601620

    申请日:2006-11-20

    IPC分类号: G06F19/00 C12Q1/37

    CPC分类号: G01N33/6845

    摘要: Provided are a method and system for verifying a protein-protein interaction according to a text mining method. The method includes extracting protein-protein interaction information from protein-related documents searched for from a bio-information document database, according to a text mining method, mapping the protein-protein interaction information to corresponding ontology identifications, and filtering the mapped protein-protein interaction information according to a frequency of the information and an impact factor of a corresponding protein-related document in order to obtain highly-weighted information.

    摘要翻译: 提供了一种根据文本挖掘方法验证蛋白质 - 蛋白质相互作用的方法和系统。 该方法包括从生物信息文献数据库中搜索的蛋白质相关文献中提取蛋白质 - 蛋白质相互作用信息,根据文本挖掘方法,将蛋白质 - 蛋白质相互作用信息映射到相应的本体标识,并过滤映射的蛋白质 - 蛋白质 根据信息的频率和相应的蛋白质相关文献的影响因子的交互信息,以获得高度加权的信息。

    Method and apparatus for predicting regulation of multiple transcription factors
    6.
    发明申请
    Method and apparatus for predicting regulation of multiple transcription factors 审中-公开
    用于预测多种转录因子调节的方法和装置

    公开(公告)号:US20070134705A1

    公开(公告)日:2007-06-14

    申请号:US11634922

    申请日:2006-12-07

    申请人: Ho Jung Ji Kim Seon Park

    发明人: Ho Jung Ji Kim Seon Park

    IPC分类号: C12Q1/68 G06F19/00

    CPC分类号: G16B25/00 G16B40/00 G16B45/00

    摘要: Provided are a method and apparatus for predicting a regulation of multiple transcription factors which can predict a regulation correlation between the multiple transcription factors and a target gene, wherein the regulation correlation is used in a method of manipulating a gene inside an actual cell. The method includes: separating gene expression profile data into expression profile data of a gene which expresses a transcription factor and an expression profile data of a target gene; clustering all pairs which can be combined, one pair including one transcription factor and one target gene; showing a result of the clustering using an interval graph; and calculating a optimum subset of the transcription factors, which occupies the maximum expression section of the target gene with the minimum number of transcription factors.

    摘要翻译: 提供了一种用于预测可以预测多种转录因子与靶基因之间的调节相关性的多种转录因子的调节的方法和装置,其中所述调节相关性用于操纵实际细胞内的基因的方法。 该方法包括:将基因表达谱数据分离为表达转录因子的基因和靶基因的表达谱数据的表达谱数据; 聚合可以组合的所有对,一对包括一个转录因子和一个靶基因; 使用间隔图显示聚类的结果; 并计算转录因子的最佳子集,其以最少数量的转录因子占据靶基因的最大表达部分。

    Apparatus and method for searching for protein active site
    7.
    发明申请
    Apparatus and method for searching for protein active site 审中-公开
    用于搜索蛋白质活性位点的装置和方法

    公开(公告)号:US20070136004A1

    公开(公告)日:2007-06-14

    申请号:US11637812

    申请日:2006-12-13

    IPC分类号: G06F19/00

    CPC分类号: G16B15/00

    摘要: An apparatus and method for searching for a protein active site by using a bottom-hat transformation are provided. First, an image of protein surface is generated and then a volumetric image is generated by sampling the protein surface in units of a predetermined length. Thereafter a morphology process is performed on the volumetric image, thereby extracting the protein active site from the morphology-processed volumetric image. Accordingly, it is possible to rapidly search for a protein active site in a 3D structural space.

    摘要翻译: 提供了一种通过使用底帽转换来搜索蛋白质活性位点的装置和方法。 首先,产生蛋白质表面的图像,然后通过以预定长度为单位对蛋白质表面进行取样来产生体积图像。 此后,对体积图像进行形态学过程,从而从形态学处理的体积图像中提取蛋白质活性位点。 因此,可以在3D结构空间中快速搜索蛋白质活性位点。

    Method of generating database schema to provide integrated view of dispersed data and data integrating system
    8.
    发明申请
    Method of generating database schema to provide integrated view of dispersed data and data integrating system 审中-公开
    生成数据库模式以提供分散数据和数据集成系统的集成视图的方法

    公开(公告)号:US20060136452A1

    公开(公告)日:2006-06-22

    申请号:US11184623

    申请日:2005-07-19

    IPC分类号: G06F17/00

    CPC分类号: G06F16/84 G06F16/211

    摘要: A method for generating a database schema in order to generate an integrated view capable of obtaining desired data from data resources dispersed and stored in different formats in different locations, and an data integrating system are provided. The method includes rules for parsing the structure and contents of an database described in a specification language, generating a schema semantically corresponding to the database, and defining data items required for generating an integrated view. Also, in order to generate a global schema expressing an integrated view, part of XQuery grammar is introduced for local schemas expressing a single database, and a definition of standard expression for expressing a data view is included. Accordingly, an data integrating system can generate an integrated view for a variety of heterogeneous databases dispersed on a network by using a specification language, and post a query in real time.

    摘要翻译: 一种用于生成数据库模式的方法,以便产生能够从不同位置以不同格式分散和存储的数据资源获得所需数据的集成视图,以及数据集成系统。 该方法包括用于解析在规范语言中描述的数据库的结构和内容的规则,生成与数据库对应的语义模式,以及定义生成集成视图所需的数据项。 此外,为了生成表达集成视图的全局模式,引入了表示单个数据库的本地模式的XQuery语法的一部分,并且包括用于表达数据视图的标准表达式的定义。 因此,数据集成系统可以通过使用规范语言生成分散在网络上的各种异构数据库的集成视图,并实时发布查询。

    System for and method of extracting and clustering information
    10.
    发明申请
    System for and method of extracting and clustering information 有权
    提取和聚类信息的系统和方法

    公开(公告)号:US20070136277A1

    公开(公告)日:2007-06-14

    申请号:US11635447

    申请日:2006-12-07

    IPC分类号: G06F17/30

    摘要: Provided is a system for and method of extracting and clustering information. The system includes a clustering criterion designing unit that reconstructs a plurality of clustering criteria for each layer or applies weights to the plurality of clustering criteria in order to design a new clustering criterion, an input data processing unit that extracts characteristics from input data according to the new clustering criterion, and a clustering unit that performs clustering on the extracted characteristics.

    摘要翻译: 提供了一种提取和聚类信息的系统和方法。 该系统包括:聚类标准设计单元,其针对每个层重建多个聚类准则或对多个聚类准则应用权重,以设计新的聚类准则;输入数据处理单元,根据输入数据从输入数据中提取特征 新的聚类准则,以及对提取的特征进行聚类的聚类单元。