System, tools and methods for viewing textual documents, extracting knowledge therefrom and converting the knowledge into other forms of representation of the knowledge
First Claim
Patent Images
1. A tool providing interactive capabilities for user involvement in extracting and disambiguating biological information in text, said tool comprising:
- a text viewer into which at least a portion of a textual document may be imported and viewed;
means for text mining the at least a portion of a textual document having been imported into the text viewer;
a list-based text editor that lists entities and interactions having been identified by said means for text mining; and
means for assigning directionality to the listed interactions.
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Accused Products
Abstract
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.
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Citations
75 Claims
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1. A tool providing interactive capabilities for user involvement in extracting and disambiguating biological information in text, said tool comprising:
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a text viewer into which at least a portion of a textual document may be imported and viewed;
means for text mining the at least a portion of a textual document having been imported into the text viewer;
a list-based text editor that lists entities and interactions having been identified by said means for text mining; and
means for assigning directionality to the listed interactions. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19)
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20. A tool providing interactive capabilities for user involvement in extracting and disambiguating biological information in text, said tool comprising:
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a text viewer into which at least a portion of a textual document may be imported and viewed;
means for text mining the at least a portion of a textual document having been imported into the text viewer;
a list-based text editor that lists entities and interactions having been identified by said means for text mining;
a canvas area for diagrammatically representing said entities and interactions; and
means for populating diagrammatic renderings on said canvas with one or more of said entities and interactions identified by said means for text mining. - View Dependent Claims (21, 22, 23, 24, 25, 26, 27, 28, 29)
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30. A tool for building biological networks of interactions from text, said tool comprising:
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a text viewer into which at least a portion of a textual document may be imported and viewed;
means for text mining the at least a portion of a textual document having been imported into the text viewer;
a list-based text editor that lists entities and interactions having been identified by said means for text mining;
means for assigning directionality to the listed interactions; and
means for selecting interactions and associated entities in the list-based editor, merging common entities and displaying a resulting network of the interactions in a window of said text view or in a separate network viewer. - View Dependent Claims (31)
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32. A tool for comparing extracted biological knowledge extracted from text, against an existing biological diagram, said tool comprising:
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a text viewer into which at least a portion of a textual document may be imported and viewed;
means for text mining the at least a portion of a textual document having been imported into the text viewer;
a list-based text editor that lists entities and interactions having been identified by said means for text mining;
a diagram viewer and means for importing at least a portion of an existing biological diagram into said diagram viewer;
means for overlaying the identified entities and interactions on said at least a portion of an existing biological diagram that is displayed in said diagram viewer;
and means for visually distinguishing the overlaid entities and interactions from a remainder of the displayed biological diagram. - View Dependent Claims (33, 34, 35, 36, 37)
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38. A method of providing interactive capabilities for user involvement in extracting and disambiguating biological information in text, said method comprising the steps of:
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importing at least a portion of a textual document into a text viewer;
text mining the at least a portion of a textual document to identify biological entities and interactions;
listing the identified entities and interactions in a list-based text editor; and
assigning directionality to the listed interactions by associating listed entities as affectors or affecteds with respect to the interactions. - View Dependent Claims (39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60)
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61. A method of providing interactive capabilities for user involvement in extracting and disambiguating biological information in text to be used in generating a biological diagram, said method comprising the steps of:
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importing at least a portion of a textual document into a text viewer;
text mining the at least a portion of a textual document to identify biological entities and interactions;
listing the identified entities and interactions in a list-based text editor;
providing a canvas area for diagrammatically representing entities and interactions having been identified by said text mining; and
populating a diagrammatic rendering on the canvas with one or more of said entities and interactions identified by said means for text mining, including indicating directionality of at least one interaction represented by the diagrammatic rendering;
wherein, upon populating the diagrammatic rendering, assignments of roles played by entities populating said diagrammatic rendering are automatically assigned in a list displayed by said list-based text editor. - View Dependent Claims (62)
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63. A method for building biological networks of interactions from text, said method comprising the steps of:
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importing at least a portion of a textual document into a text viewer;
text mining the at least a portion of a textual document having been imported into the text viewer;
listing entities and interactions having been identified by said text mining;
assigning directionality to the listed interactions; and
selecting interactions and associated entities and displaying a resulting network of the interactions and entities. - View Dependent Claims (64, 65, 66, 67)
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68. A computer readable medium carrying one or more sequences of instructions for user involvement in extracting and disambiguating biological information in text to be used in generating a biological diagram, wherein execution of one or more sequences of instructions by one or more processors causes the one or more processors to perform the steps of:
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importing at least a portion of a textual document into a text viewer;
text mining the at least a portion of a textual document to identify biological entities and interactions;
listing the identified entities and interactions in a list-based text editor; and
assigning directionality to the listed interactions by associating listed entities as affectors or affecteds with respect to the interactions. - View Dependent Claims (69, 70, 71, 72, 73, 74, 75)
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Specification