ASSOCIATION OF DATA TO A BIOLOGICAL SEQUENCE

• US 20140089329A1
• Filed: 11/29/2012
• Published: 03/27/2014
• Est. Priority Date: 09/27/2012
• Status: Active Grant

• Current Assignee: International Business Machines Corporation
• Original Assignee: International Business Machines Corporation
• Inventors: Kozloski, James R., Pickover, Clifford A., Wubben, Jacinta M., Zhou, Ruhong
• Granted Patent: US 9,311,360 B2
• Time in Patent Office: Days
• US Class Current: 707/749
• CPC Class Codes: G06F 16/24578 using ranking
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids

Abstract

A method for associating data with a target biological sequence includes identifying, in a network, one or more references to data, where the data has a relevance level greater than a predetermined threshold. The method includes associating the one or more references to one or more probe sequences corresponding to a segment of a biological sequence to which the data pertains The one or more probe sequences are ranked based on one or more criteria and the probe sequences are assigned a level of affinity to a segment of the target biological sequence based at least on the ranking of each reference.

Claims

1. A method for associating data with a target biological sequence, comprising:

identifying, in a network, one or more references to data, the data having a relevance level greater than a predetermined threshold;

associating, by a processor, the one or more references to one or more probe sequences corresponding to a segment of a biological sequence to which the data pertains;

ranking, by the processor, the one or more probe sequences based on one or more criteria; and

assigning, by the processor, the one or more probe sequences with a level of affinity to a segment of the target biological sequence based at least on the ranking of each reference.

2. The method of claim 1, wherein the references are uniform resource locators (URLs).

3. The method of claim 1, wherein identifying the one or more references having a relevance level greater than a predetermined threshold includes analyzing the one or more references to detect the presence of one or more of key words, phrases, symbols and sources of the one or more references.

4. The method of claim 1, wherein associating each reference to a probe sequence corresponding to a segment of a biological sequence includes associating each reference with a biological sequence that is complementary to the segment of the biological sequence to which the data pertains.

5. The method of claim 1, wherein ranking the one or more probe sequences comprises determining a similarity between each probe sequence and the biological sequence to which the reference pertains, and

ranking the one or more probe sequences further comprises at least one of determining an importance of a source of each reference, determining a popularity of each reference, and determining a historical applicability of each reference to the biological sequence to which the reference pertains.

6. The method of claim 5, wherein determining the similarity between each reference and the biological sequence to which the reference pertains includes determining a match between each reference a complement of the biological sequence.

7. The method of claim 6, wherein the data includes at least one of a document, an analysis tool, and biographical information, the method further comprising associating the one or more probe sequences with at least one of the document, the analysis tool, and the biographical information.

8. The method of claim 7, wherein determining an importance of a source of each reference includes at least one of determining a number of citations of an author of the document, determining an organization to which an author of the document belongs, and determining a type of analysis performed by the analysis tool,

determining a popularity of each reference includes at least one of determining a number of citations of the document and a frequency of use of the analysis tool, and

determining a historical applicability of each reference to the biological sequence to which the reference pertains includes at least one of determining a frequency with which the document has been cited in association with the biological sequence and determining a frequency with which the analysis tool has been used to analyze the biological sequence.

9. The method of claim 6, wherein the at least one probe sequence includes two or more probe sequences corresponding to a same segment of the target biological sequence, and

assigning the two or more probe sequences with a level of affinity to the same segment of the target biological sequence includes competitively comparing the two or more probe sequences such that a probe sequence having a higher ranking is assigned a higher level of affinity than a probe sequence having a lower ranking.

10. The method of claim 1, further comprising displaying a graphical representation of the segment of the target biological sequence on a display;

and

displaying a graphical representation of the level of affinity of each probe sequence to the segment of the target biological sequence on the display by adjusting a physical distance of a graphical representation of the probe sequence from the graphical representation of the segment based on the level of affinity of the probe sequence.

11. The method of claim 1, further comprising:

associating a first one of the two or more references with a first probe sequence based on the level of affinity to the segment of the biological sequence; and

simulating annealing of a second probe sequence representing data in the network to the first probe sequence based on a determined affinity of the second probe sequence to the first probe sequence.

12. A method for simulating annealing with a biological sequence, comprising:

identifying a target biological sequence;

identifying a plurality of references to data in a network as being relevant references based on a determination that the plurality of references have a relevance level greater than a threshold relevance level;

associating the relevant references with at least one segment of the target biological sequence; and

ranking the relevant references based on predetermined criteria to determine a level of affinity of the relevant references with the at least one segment of the target biological sequence.

13. The method of claim 12, wherein identifying the target biological sequence includes identifying a biological sequence selected by a user in a host computer connected to the network.

14. The method of claim 13, wherein the biological sequence is selected by displaying a graphical representation of the biological sequence on a display device.

15. The method of claim 12, wherein identifying the plurality of references to data as being relevant references includes detecting the presence of one or more of key words, phrases, symbols and sources of the data referred to by the plurality of references.

16. The method of claim 12, wherein the plurality of references are uniform resource locators (URLs).

17. The method of claim 12, wherein associating the relevant references with at least one segment of the target biological sequence includes associating the relevant references with probe sequences corresponding to the at least one segment of the target biological sequence.

18. The method of claim 17, wherein the probe sequences include a sequence of nucleotides complementary to a sequence of nucleotides of the at least one segment of the target biological sequence.

19. The method of claim 12, wherein ranking the relevant references based on the predetermined criteria includes ranking the relevant references based on a correspondence between the relevant and the at least one segment of the target biological sequence, and ranking the relevant references based on at least one of an importance of a source of data referred to by the relevant references, a popularity of the data referred to by the relevant references, and a historical applicability of the data referred to by the relevant references to the at least one segment of the target biological sequence.

20. The method of claim 19, wherein the data includes an analysis tool relevant to the segment of the biological sequence,

the importance of the source of data referred to by the relevant references is based on at least one of a source of the analysis tool and a type of analysis performed by the analysis tool,

a popularity of data referred to by the relevant references is based on a frequency of use of the analysis tool, and

a historical applicability of data referred to by the relevant references is based on a frequency with which an analysis tool has been used to analyze the segment of the target biological sequence.

21. The method of claim 19, wherein the data includes a document relevant to the at least one segment of the target biological sequence,

the importance of the source of data referred to by the relevant references is based on at least one of a number of citations of an author of the document and an organization with which the author of the document is associated,

a popularity of data referred to by the relevant references is based on at least one of a number of citations to the document, and

a historical applicability of data referred to by the relevant references is based on a frequency with which the document has been cited in association with the segment of the biological sequence.

22. The method of claim 12, further comprising:

displaying a graphical representation of the at least one segment of the target biological sequence on a display and a graphical representation of the level of affinity of the relevant references to the at least one segment of the target biological sequence on the display by adjusting a physical distance of a graphical representation of the relevant references from the graphical representation of the segment based on the level of affinity of the relevant references.

23. The method of claim 22, wherein the at least one segment of the target biological sequence is displayed as a helix and the graphical representations of the relevant references are located at varying distances from the helix based on varying levels of affinity of the respective relevant references.

24. The method of claim 22, wherein displaying the graphical representation of the at least one segment of the target biological sequence includes displaying a plurality of contiguous segments of the target biological sequence, displaying a plurality of graphical representations of relevant references located at locations along the graphical representation of the plurality of segments based on an association between a respective segment among the plurality of segments and a respective relevant reference, and displaying the plurality of graphical representations of relevant references located at different distances from the graphical representation of the plurality of segments of the target biological sequence based on determined affinities of the respective relevant references with the respective plurality of segments of the target biological sequence.