System and methods for navigating and visualizing multi-dimensional biological data

• US 7,181,373 B2
• Filed: 08/13/2004
• Issued: 02/20/2007
• Est. Priority Date: 08/13/2004
• Status: Expired due to Fees

• Current Assignee: Agilent Technologies, Inc.
• Original Assignee: Agilent Technologies, Inc.
• Inventors: Le Cocq, Christian A., Grimm, Rudolf
• Primary Examiner(s): PALADINI, ALBERT WILLIAM
• Application Number:
  US10/918,598
• Publication Number:
  US 20060036425A1
• Time in Patent Office: 921 Days
• Field of Search: 703/1, 382298-300, 358/1.2, 700/98, 348/208.06
• US Class Current: 703/1
• CPC Class Codes: G06T 11/206 Drawing of charts or graphs
• CPC Class Codes: G06T 2210/36 Level of detail
• CPC Class Codes: G16B 45/00 ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks

Abstract

Methods systems and computer readable media for manipulating and displaying sparse data contained within very large datasets. Particular applications includes those to proteomics and metabolomics. Navigation of the large data sets from a global perspective may be practically implemented, so that a user is not confined to a narrow slice of data at a time, thus providing context of the whole dataset while viewing data within the dataset.

Claims

1. A method for displaying and manipulating a large dataset to facilitate identification, correlations or other useful relationships among the data in the dataset, the method comprising the steps of:

generating a planar view of a two-dimensional projection of the data in the dataset;

continuously zooming the planar view, to provide a zoomed-in or a zoomed out view of at least a portion of the data, wherein the continuous zooming feature facilitates a user'"'"'s ability to maintain reference; and

converting an abstraction of at least a portion of the data to a different level of abstraction during said continuously zooming step when a predetermined level of zooming-in has been reached, and converting the different level of abstraction back to the abstraction of the at least a portion of the data when a predetermined level of zooming-out has been reached.

2. The method of claim 1, wherein said planar view is continuously scrollable.

3. The method of claim 1, further comprising converting a number of representations at said different level of abstraction to a second different level of abstraction during said continuously zooming step when a second predetermined level of zooming-in has been reached, and converting the second different level of abstraction back to the different level of abstraction when a second predetermined level of zooming-out has been reached.

4. The method of claim 1, further comprising seamlessly zooming the view of the entire dataset to provide varied levels of magnification of the entire dataset.

5. The method of claim 1, wherein said converting is based on computer data structures including a set of pre-computed compressed bitmaps at various magnifications and a set of pre-computed symbol locations for identifying placement of said symbolic representation.

6. The method of claim 3, further comprising performance of a predefined additional number of conversions to additional levels of abstraction.

7. The method of claim 3, wherein said representations at said different level of abstraction are symbolic representations which are symbolic of features and wherein said representation at said second different level of abstraction comprise composite symbolic representations of groups of said symbolic representations at the different level of abstraction.

8. The method of claim 7, wherein said converting a number of said symbolic representations to a composite symbolic representation at said second different level of abstraction comprises merging said symbolic representations at the different level of abstraction into said composite symbolic representation at the second different level of abstraction, wherein said composite symbolic representation represents said symbolic representations.

9. The method of claim 1, wherein the step of continuously zooming is performed in at least one dimension selected from the group consisting of:

horizontal dimension, vertical dimension, and both horizontal and vertical dimensions.

10. The method of claim 1, wherein said continuously zooming comprises updating the planar view via sub-sampling of the data provided in a detailed bitmap representation.

11. The method of claim 10, wherein said sub-sampling comprises selecting a pixel having the maximum intensity, relative to all other pixels sampled in the sub-sample, and representing the sub-sampled group of pixels with the intensity of the selected pixel.

12. The method of claim 1, wherein said continuous zooming comprises merging a multiplicity of symbolic representations into a composite symbol representative of the multiplicity of symbolic representations.

13. The method of claim 1, wherein the large dataset comprises mass spectrometry data.

14. The method of claim 13, wherein said mass spectrometry data is represented by intensity values per Dalton per time unit.

15. The method of claim 1, wherein the data is sparsely distributed in the large dataset.

20. The method of claim 1, further comprising the steps of:

selecting a feature in the view of the data; and

entering at least one annotation that is to be associated with said selected feature of the data.

21. The method of claim 20, wherein said selection is accomplished via lassoing said feature with mouse movement.

22. The method of claim 20, wherein said selection is accomplished via mouse click.

23. The method of claim 20, wherein said entering of at least one annotation is accomplished via an object editor interface.

24. The method of claim 20, wherein said entering of at least one annotation is accomplished via free-form sketching.

25. The method of claim 20, wherein said entering of at least one annotation is accomplished via attachment of an external data file.

26. The method of claim 20, further comprising overlaying at least one of said entered annotations on said view of the data.

27. The method of claim 1, wherein said data comprises mass spectrometry data.

28. The method of claim 1, wherein said data comprises biological data.

29. The method of claim 1, wherein said data comprises chemical data.

30. The method of claim 1, further comprising selecting a portion of the data and automatically querying at least one database, based on the selection made.

31. The method of claim 30, wherein said database query triggers display of retrieved data in an associated viewer software.

32. The method of claim 31, wherein selection of a segment of said data in said associated viewer software triggers scrolling to display a set of features in said data that correspond to said segment of data in said associated viewer.

33. A method comprising forwarding a result obtained from the method of claim 1 to a remote location.

34. A method comprising transmitting data representing a result obtained from the method of claim 1 to a remote location.

35. A method comprising receiving a result obtained from a method of claim 1 from a remote location.

16. A method for comparing multiple, large scale datasets, comprising the steps of

fitting equal scales and origins to views of each large scale dataset to be compared, so that a reference to a location on a view of one of the views points to the same corresponding location on all other views;

overlaying said views on one display; and

visually representing data in each said view to visually distinguish from corresponding data in all other views.

17. The method of claim 16, wherein said visually representing comprises color-coding.

18. The method of claim 16, wherein said large scale datasets comprise mass spectrometry data.

19. The method of claim 17, wherein said color-coding comprises mapping a signal intensity value of a data point from one of said large scale datasets to a scale of intensity values assigned to a range of colors.

36. A system for displaying and manipulating data to facilitate identification, correlations or other useful relationships among the data, said system comprising:

means for generating a planar view of a 2-D projection of the data, which is continuously zoomable and scrollable,

means for reducing raw data to symbols representative of said raw data.

37. A system for comparing multiple data sets, comprising

means for fitting a scale and origin of one data set view set onto views of all other data sets of the multiple data sets, to provide windows on all of the data sets pointing to homologous locations,

means for color-coding said fitted data sets to visually distinguish said fitted data sets from each other;

and

means for overlaying the color-coded, fitted, multiple data set views on a single window.

38. A computer readable medium carrying one or more sequences of instructions for displaying and manipulating data to facilitate identification, correlations or other useful relationships among the data, 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:

generating a planar view of a 2-D projection of the data, which is continuously zoomable and scrollable.