Cooperation-based method of managing, displaying, and updating DNA sequence data

• US 8,990,231 B2
• Filed: 10/28/2011
• Issued: 03/24/2015
• Est. Priority Date: 10/28/2010
• Status: Expired due to Fees

• Current Assignee: Samsung SDS (China) Co., Ltd. (Samsung Group)
• Original Assignee: Samsung SDS (China) Co., Ltd. (Samsung Group)
• Inventors: Park, Minseo, Lee, Jung-Youn
• Primary Examiner(s): OBISESAN, AUGUSTINE KUNLE
• Application Number:
  US13/283,899
• Publication Number:
  US 20120110430A1
• Time in Patent Office: 1,243 Days
• Field of Search: None
• US Class Current: 707/758
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 20/20 Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• CPC Class Codes: G16B 45/00 ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: G16B 50/10 Ontologies; Annotations

Abstract

A cooperation-based method and system of managing, displaying, and updating DNA sequence data including receiving annotation data inputted by a user for an anchor corresponding to at least one base of a DNA sequence, and storing the received annotation data in an annotation data table which includes one or more columns for annotation data; receiving data about a position of an anchor which corresponds to at least one base of a DNA sequence in the DNA sequence, and displaying the position of the anchor on a DNA sequence map based on the received data; and getting input of a position at which an annotation is to be input on a DNA sequence map, displaying an annotation input interface which includes an edit region for inputting an annotation, and transmitting annotation data including annotation contents inputted through the edit region and the inputted position to a DNA sequence data storage device.

Claims

1. A cooperation-based method of managing DNA sequence data, the method comprising:

receiving annotation data inputted by a user for an anchor corresponding to at least one base of a DNA sequence;

storing the received annotation data in an annotation data table which comprises one or more columns for annotation data; and

displaying annotation contents contained in the annotation data for the anchor corresponding to the at least one base of the DNA sequence,

wherein the anchor corresponding to the at least one base of the DNA sequence is displayed on a DNA sequence map,

wherein the received annotation data inputted by the user for the anchor corresponding to the at least one base of the DNA sequence comprises at least one of an experimental results memo, a reply to an existing annotation, or a correction/opinion regarding an existing annotation,

wherein the columns for the annotation data comprise a contents column which stores a character string representing the content of an annotation and at least one of an annotation type column which stores one of pre-designated annotation types, an annotation evaluation value column which stores an evaluation value calculated based on evaluations by users other than an annotation author, or a keyword column which stores information about a keyword extracted from the character string by comparing the character string with a keyword dictionary, and

wherein the displaying of the annotation contents contained in the annotation data for the anchor comprises, when two or more annotations exist for the anchor, arranging and displaying the annotations according to scores calculated based on a similarity between a job of the user and that of an annotation author contained in the annotation data, the similarity between interests of the user and those of the annotation author contained in the annotation data, and an evaluation value of the annotation data.

2. A cooperation-based method of displaying DNA sequence data, the method comprising:

receiving data about a position of each of at least one anchor, which corresponds to at least one base of a DNA sequence, in the DNA sequence;

displaying the position of each of the at least one anchor on a DNA sequence map based on the received data;

receiving annotation data for the at least one anchor;

receiving information about one or more selected anchors; and

displaying annotation contents contained in annotation data for the one or more selected anchors on the DNA sequence map,

wherein the annotation contents comprise at least one of an experimental results memo, a reply to an existing annotation, or a correction/opinion regarding an existing annotation,

wherein the displaying of the annotation contents contained in the annotation data for the one or more selected anchors comprises, when two or more annotations exist for each of the one or more selected anchors, arranging and displaying the annotations according to scores calculated based on the similarity between a job of a current user and that of an annotation author contained in the annotation data, the similarity between interests of the current user and those of the annotation author contained in the annotation data, and an evaluation value of the annotation data.

3. The cooperation-based method of claim 2, further comprising:

grouping the at least one anchor based on a keyword included in annotation contents contained in the annotation data and displaying the grouped anchors on the DNA sequence map.

4. The cooperation-based method of claim 2,

wherein the annotation data comprises author information, annotation type information, evaluation value information, and the annotation contents;

and

further comprising filtering the annotation data based on at least one of the author information, the annotation type information, the evaluation value information, or the annotation contents and displaying the filtered annotation data.

5. The cooperation-based method of claim 4, wherein the filtering of the annotation data and the displaying of the filtered data comprises filtering the annotation data using values calculated based on the similarity between a job of a current user and that of an annotation author contained in the annotation data and the similarity between interests of the current user and those of the annotation author contained in the annotation data and displaying the filtered annotation data.

6. A cooperation-based method of updating DNA sequence data, the method comprising:

getting input of a position, at which an annotation is to be input, on a DNA sequence map, the position corresponding to at least one base on the DNA sequence map;

displaying an annotation input interface which comprises an edit region for inputting an annotation;

transmitting annotation data comprising annotation contents inputted through the edit region and the inputted position to a DNA sequence data storage device; and

displaying the annotation contents contained in the annotation data for the position corresponding to the at least one base on the DNA sequence map,

wherein the annotation contents inputted through the edit region correspond to the at least one base on the DNA sequence map and comprise at least one of an experimental results memo, a reply to an existing annotation, or a correction/opinion regarding an existing annotation, and

wherein the displaying of the annotation contents contained in the annotation data for the position comprises, when two or more annotations exist for the position, arranging and displaying the annotations according to scores calculated based on a similarity between a job of a current user and that of an annotation author contained in the annotation data, the similarity between interests of the current user and those of the annotation author contained in the annotation data, and an evaluation value of the annotation data.

7. The cooperation-based method of claim 6, wherein the displaying the annotation input interface comprises displaying the annotation input interface which further comprises an annotation type selection region, and the transmitting annotation data storage device comprises transmitting annotation data, which further comprise an annotation type selected through the annotation type selection region, to the DNA sequence data storage device.

8. The cooperation-based method of claim 7, wherein the getting input of a position comprises getting input of a position of one of anchors shown on the DNA sequence map, the displaying of the annotation input interface comprises displaying the annotation input interface which further comprises an evaluation selection region for selecting an evaluation of an existing annotation when the selected annotation type is a reply type to the existing annotation, and the transmitting annotation data comprises transmitting information about the evaluation of the existing annotation selected through the evaluation selection region to the DNA sequence data storage device.

9. The cooperation-based method of claim 6, further comprising getting input for designating whether to make the inputted annotation contents public.

10. A cooperation-based system for managing DNA sequence data, the system comprising:

a database (DB) server storing annotation data for an anchor, wherein the anchor corresponds to at least one base of a DNA sequence, and DNA sequence data; and

a service server transmitting a portion of the annotation data and a portion of the DNA sequence data corresponding to an area requested by a client, to the client, receiving annotation data for an anchor comprising position information of the anchor from the client, processing the received annotation data into an annotation data format, and storing the processed annotation data in the DB server,

wherein the received annotation data corresponds to the at least one base of the DNA sequence and comprises at least one of an experimental results memo, a reply to an existing annotation, or a correction/opinion regarding an existing annotation,

wherein the annotation data comprise a contents which stores a character string representing the content of an annotation, and at least one of an annotation type which stores one of pre-designated annotation types, an annotation evaluation value which stores an evaluation value calculated based on evaluations by users other than an annotation author, or a keyword which stores information about a keyword extracted from the character string by comparing the character string with a keyword dictionary, and

wherein the service server, in the transmitting the portion of the annotation data and the portion of the DNA sequence data corresponding to the area requested by the client, when two or more annotations exist for the anchor, arranges the annotations for display according to scores calculated based on a similarity between a job of a current user and that of an annotation author contained in the annotation data, the similarity between interests of the current user and those of the annotation author contained in the annotation data, and an evaluation value of the annotation data.

11. The cooperation-based system of claim 10, further comprising the client receiving the portion of the annotation data and the portion of the DNA sequence data from the service server, displaying a DNA sequence map on which position of the anchor contained in the portion of the annotation data are shown, getting input of position information of an anchor and annotation contents for the anchor from a user, and transmitting the inputted position information and annotation contents to the service server.

12. The cooperation-based system of claim 11, wherein the client groups the anchors based on a keyword included in annotation contents contained in the portion of the annotation data and displays the grouped anchors on the DNA sequence map.