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1. 发明申请

US20070174019A1 Network-based approaches to identifying significant molecules based on high-throughput data analysis 审中-公开
标题翻译：基于网络的基于高通量数据分析识别重要分子的方法
公开(公告)号：US20070174019A1
公开(公告)日：2007-07-26
申请号：US11264259
申请日：2005-10-31
申请人： Aditya Vailaya , Allan Kuchinsky , Euan Ashley , Jennifer King , Rossella Ferrara , Thomas Quertermous
发明人： Aditya Vailaya , Allan Kuchinsky , Euan Ashley , Jennifer King , Rossella Ferrara , Thomas Quertermous
IPC分类号： G06F17/18
CPC分类号： G16B5/00 , G16B20/00
摘要： Methods, systems and computer readable media for network-based identification of significant molecules, for which at least one biological network is provided to include significant molecules to be identified. A node in the network is identified. A member-specific sub-network containing nodes connected to the identified node is identified for L levels of nearest neighbors, wherein L is a positive integer, and a connectivity score is calculated for the molecule represented by the identified node based on significance scores of each node contained in the member-specific sub-network. These steps are repeated for other nodes in the network. Methods, systems and computer readable media for network-based identification of significant molecules, for which at least one biological network is provided to include significant molecules to be identified, a data set including data values characterizing molecules experimented on is provided, and an interesting list of molecules is provided as a subset of the molecules from the dataset, the interesting list including significance scores for the molecules in the list. Such identification includes identifying a node in the network; identifying a member-specific sub-network containing nodes connected to the identified node for L levels of nearest neighbors, wherein L is a positive integer; extracting the member-specific sub-network from the network; and repeating these steps for each of the other nodes in the network that corresponds to a molecule in the interesting list.
摘要翻译：用于基于网络识别重要分子的方法，系统和计算机可读介质，其中提供至少一个生物网络以包括要识别的重要分子。识别网络中的节点。针对L个最近邻的L个级别识别包含连接到所识别节点的节点的成员特定子网络，其中L是正整数，并且基于由所识别的节点表示的分子计算连通性得分，基于每个节点包含在成员特定子网中。对网络中的其他节点重复这些步骤。提供用于基于网络识别显着分子的方法，系统和计算机可读介质，其中提供至少一个生物网络以包括要识别的重要分子，提供包括表征实验分子的数据值的数据集，以及有趣的列表的分子作为来自数据集的分子的子集提供，有趣的列表包括列表中分子的显着性得分。这种识别包括识别网络中的节点; 识别包含连接到所识别的节点的节点的成员特定子网络用于最近邻的L级，其中L是正整数; 从网络中提取成员专用子网; 并且对于与有趣列表中的分子相对应的网络中的每个其他节点重复这些步骤。

2. 发明申请

US20050278321A1 Systems, methods and computer readable media for performing a domain-specific metasearch, and visualizing search results therefrom 失效
标题翻译：用于执行域特定元搜索的系统，方法和计算机可读介质，以及从其中可视化搜索结果
公开(公告)号：US20050278321A1
公开(公告)日：2005-12-15
申请号：US11166696
申请日：2005-06-24
申请人： Aditya Vailaya , Allan Kuchinsky , Robert Kincaid
发明人： Aditya Vailaya , Allan Kuchinsky , Robert Kincaid
IPC分类号： G06F7/00 , G06F19/28
CPC分类号： G06F17/30864 , G06F17/30991 , G06F19/28 , Y10S707/99935 , Y10S707/99943
摘要： Systems, methods and computer readable media for performing a domain-specific metasearch, and obtaining search results therefrom. A metasearch engine capable of accessing generic, web-based search engines and domain-relevant search engines is provided to receive one or more queries inputted by a user, and to search for documents on at least one the generic, web-based search engines and domain-relevant search engines which are relevant to the queries. Raw data search results are fetched in the form of text documents. Relevant data including semantic information are extracted from the raw data search results, and converted to a local format. The relevant data having been converted to the local format may be visualized as a network visualization. Additionally or alternatively, the raw data search results may be ranked and/or filtered based on the linking of the relevant data. Visualization of the raw data having been ranked and/or filtered may be performed in addition to, or alternative to visualization of the network.
摘要翻译：用于执行域特定元搜索的系统，方法和计算机可读介质，以及从其获得搜索结果。提供了能够访问通用的，基于网络的搜索引擎和域相关搜索引擎的元搜索引擎，用于接收用户输入的一个或多个查询，并且在至少一个通用的基于web的搜索引擎上搜索文档，以及与查询相关的域相关搜索引擎。原始数据搜索结果以文本文档的形式提取。从原始数据搜索结果中提取包括语义信息的相关数据，并将其转换为本地格式。已经转换为本地格式的相关数据可以被可视化为网络可视化。另外或替代地，可以基于相关数据的链接对原始数据搜索结果进行排名和/或过滤。已经排序和/或过滤的原始数据的可视化可以除了网络的可视化之外或替代以进行。

3. 发明申请

US20050039123A1 Method and system for importing, creating and/or manipulating biological diagrams 审中-公开
标题翻译：导入，创建和/或操纵生物图的方法和系统
公开(公告)号：US20050039123A1
公开(公告)日：2005-02-17
申请号：US10641492
申请日：2003-08-14
申请人： Allan Kuchinsky , Aditya Vailaya , Robert Kincaid , Peter Bluvas , Annette Adler , David Moh , Carl Myerholtz
发明人： Allan Kuchinsky , Aditya Vailaya , Robert Kincaid , Peter Bluvas , Annette Adler , David Moh , Carl Myerholtz
IPC分类号： G06F19/00 , G06T11/20 , G06F17/21
CPC分类号： G06T11/206 , G16B5/00 , G16B45/00
摘要： Systems, methods and recordable media for interactively importing, creating, and manipulating biological diagrams. Such diagrams may be used for linking and navigating to other sources of biological information. Such diagrams may also be used interactively with other diagrams or other views of biological knowledge
摘要翻译：用于交互式导入，创建和操纵生物图的系统，方法和可记录介质。这样的图可以用于链接和导航到其他生物信息来源。这些图也可以与其他图或其他生物学知识的观点交互使用

4. 发明授权

US07224362B2 Systems and methods for providing visualization and network diagrams 失效
标题翻译：提供可视化和网络图的系统和方法
公开(公告)号：US07224362B2
公开(公告)日：2007-05-29
申请号：US10356122
申请日：2003-01-30
申请人： Robert Kincaid , David Moh , Allan Kuchinsky
发明人： Robert Kincaid , David Moh , Allan Kuchinsky
IPC分类号： G06T11/20 , G09G5/00
CPC分类号： G06F3/0481 , G06F19/26
摘要： Visualization techniques tools and systems for displaying network diagrams to convey both focus and context to a user of the display. Network diagrams may be displayed to emulate a three dimensional presentation. Network diagrams may be presented with items of interest in sharp definition and the remainder of a diagram or diagrams being blurred or having relative degrees of sharpness/blurriness.
摘要翻译：可视化技术工具和系统，用于显示网络图以将焦点和上下文传达给显示器的用户。可以显示网络图以模拟三维表示。网络图可以以清晰的清晰度呈现感兴趣的项目，并且图形或图表的其余部分被模糊或具有相对的锐度/模糊程度。

5. 发明申请

US20050038770A1 System, tools and methods for viewing textual documents, extracting knowledge therefrom and converting the knowledge into other forms of representation of the knowledge 有权
标题翻译：用于查看文本文档的系统，工具和方法，从中提取知识并将知识转换为其他形式的知识表示
公开(公告)号：US20050038770A1
公开(公告)日：2005-02-17
申请号：US10642376
申请日：2003-08-14
申请人： Allan Kuchinsky , Aditya Vailaya , David Moh , Peter Bluvas
发明人： Allan Kuchinsky , Aditya Vailaya , David Moh , Peter Bluvas
IPC分类号： G06F17/22 , G06F17/27 , G06F19/00 , G06F7/00
CPC分类号： G06F17/2775 , G06F19/12 , G06F19/24 , G06F19/26 , Y10S707/99936 , Y10S707/99943
摘要： Systems, tools, methods and recordable media for text mining textual documents and extracting and associating entities and interactions mined with other data formats, such as diagrammatic displays and experimental data, using a local format. Additionally, information may be overlaid and compared with existing biological diagrams.
摘要翻译：用于文本挖掘文本文档的系统，工具，方法和可记录介质，并使用本地格式提取和关联实体以及与其他数据格式（如图形显示和实验数据）开发的交互。此外，可以将信息重叠并与现有生物图进行比较。

6. 发明申请

US20050188294A1 Systems, tools and methods for constructing interactive biological diagrams 审中-公开
标题翻译：用于构建交互式生物图的系统，工具和方法
公开(公告)号：US20050188294A1
公开(公告)日：2005-08-25
申请号：US10784523
申请日：2004-02-23
申请人： Allan Kuchinsky , Aditya Vailaya , David Moh , Peter Bluvas
发明人： Allan Kuchinsky , Aditya Vailaya , David Moh , Peter Bluvas
IPC分类号： G06F19/00 , G06T11/20 , G09B23/28 , G06F15/00 , G06F17/00
CPC分类号： G16B45/00 , G16B5/00 , G16B40/00
摘要： Systems, tools, methods and recordable media for providing a visual grammar to be associated with a local format for creating interactive biological diagrams. Stencils are provided to represent higher level representations of associated entities and interactions are descriptively and unambiguously displayed. Additionally, information may be overlaid and compared with existing biological diagrams.
摘要翻译：用于提供与本地格式相关联的视觉语法的系统，工具，方法和可记录介质，用于创建交互式生物图。提供模板以表示相关联实体的更高级别表示，并且描述性且明确地显示交互。此外，可以将信息重叠并与现有生物图进行比较。

7. 发明申请

US20050027729A1 System and methods for visualizing and manipulating multiple data values with graphical views of biological relationships 审中-公开
标题翻译：用生物学关系的图形视图来可视化和操纵多个数据值的系统和方法
公开(公告)号：US20050027729A1
公开(公告)日：2005-02-03
申请号：US10928494
申请日：2004-08-27
申请人： Allan Kuchinsky , Robert Kincaid
发明人： Allan Kuchinsky , Robert Kincaid
IPC分类号： G06F7/00 , G06F19/12 , G06F19/20 , G06F19/26
CPC分类号： G16B45/00 , G16B5/00 , G16B25/00
摘要： Methods, systems and computer readable media for visualizing multiple data values adjacent graphical representations of entities in a diagram representing biological relationships between the entities. A diagram of interconnected entities representing biological relationships between the entities is displayed. A data set having rows of data values, each row containing values representing a single entity is provided, wherein at least some of the entities are represented on the diagram. At least one row of data values from the dataset is overlaid on the displayed diagram such that the row of data values appears adjacent the entity on the diagram that matches the entity in the data set that the row of data characterizes. The display of the row of data values is scaled so that components of the display are dimensionally proportional to numerical values of the data values taken from the data set.
摘要翻译：方法，系统和计算机可读介质，用于在表示实体之间的生物关系的图中的实体的图形表示之间可视化多个数据值。显示表示实体之间的生物关系的互连实体的图。提供了具有数据值行的数据集，每行包含表示单个实体的值，其中在图中表示至少一些实体。来自数据集的至少一行数据值被覆盖在显示的图上，使得数据行的行出现在与图中数据集中表示的数据集中的实体相匹配的实体上。数据值行的显示被缩放，使得显示器的组件在尺寸上与从数据集获取的数据值的数值成比例。

8. 发明授权

US07146030B2 System and methods for extracting semantics from images 有权
公开(公告)号：US07146030B2
公开(公告)日：2006-12-05
申请号：US10155615
申请日：2002-05-22
申请人： Aditya Vailaya , Annette Marie Adler , Allan Kuchinsky
发明人： Aditya Vailaya , Annette Marie Adler , Allan Kuchinsky
IPC分类号： G06K9/00
CPC分类号： G06K9/00476 , G06F19/12 , G06F19/26
摘要： System, tools and methods for extracting the contents from a graphical image, such as the representation of a biological process, and converting the contents into a standardized, machine readable format. The standard format can be used to create editable graphical representations of images, such as biological models.

9. 发明申请

US20050197783A1 Methods and systems for extension, exploration, refinement, and analysis of biological networks 审中-公开
标题翻译：生物网络的扩展，探索，细化和分析的方法和系统
公开(公告)号：US20050197783A1
公开(公告)日：2005-09-08
申请号：US10794341
申请日：2004-03-04
申请人： Allan Kuchinsky , Aditya Vailaya , Annette Adler
发明人： Allan Kuchinsky , Aditya Vailaya , Annette Adler
IPC分类号： C12Q1/00 , G01N33/48 , G01N33/50 , G06F19/00
CPC分类号： G16B5/00 , G16B25/00 , G16B40/00
摘要： Systems, methods and recordable media for facilitating user-guidance of computational analysis and knowledge extraction tools for use with biological data for disambiguation and determination of causation in representations of the data. Systems, methods, tools and computer readable media for user-guided expansion of biological networks and manipulations of the same. Tools for qualitative simulation of network models, for identifying interactions between multiple networks and form maintaining knowledge about multiple alternative biological networks. Combinations of portions of networks may be constructed to provide optimal networks. Networks may be evaluated against experimental data and networks of interest may be identified based on experimental data.
摘要翻译：系统，方法和可记录介质，用于促进计算分析和知识提取工具的用户指导，以便与生物数据一起使用，以消除歧义和确定数据表示中的因果关系。用于用户引导扩展生物网络的系统，方法，工具和计算机可读介质及其操作。用于网络模型的定性模拟的工具，用于识别多个网络之间的交互并形成维护关于多个替代生物网络的知识。可以构建网络的部分的组合以提供最佳网络。可以根据实验数据评估网络，并且可以基于实验数据来识别感兴趣的网络。

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