Method for verifying biodata, and apparatus therefor

• US 10,528,531 B2
• Filed: 07/18/2013
• Issued: 01/07/2020
• Est. Priority Date: 12/03/2012
• Status: Active Grant

• Current Assignee: KT Corporation
• Original Assignee: KT Corporation
• Inventors: Hong, Chang-Bum, Lee, Mi-Sook, Choi, Han-Kyu, Choi, Dae-Chul
• Primary Examiner(s): Woitach, Joseph
• Application Number:
  US14/649,546
• Publication Number:
  US 20170147614A1
• Time in Patent Office: 2,364 Days
• Field of Search: None
• CPC Class Codes: G06F 11/08 Error detection or correction by redundancy in data representation, e.g. by using checking codes
• CPC Class Codes: G06F 16/215 Improving data quality; Data cleansing, e.g. de-duplication, removing invalid entries or correcting typographical errors
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: G16B 50/50 Compression of genetic data

Abstract

The present disclosure relates to a method and an apparatus for verifying biodata by verifying, in real-time, whether there are errors in biodata received from a client terminal. The method may include the steps of: receiving a request to upload biodata from the client terminal and storing the biodata to a storage system; extracting sequences from the biodata and verifying whether the sequences are valid data; upon detection of errors in a sequence, calculating an error ratio of the sequence and, when the calculated error ratio exceeds a threshold value, terminating the upload of the biodata.

Claims

1. A method for verifying biodata received from a client terminal by a data verification apparatus including at least one processor, the method comprising:

receiving a portion of biodata uploaded through a network from the client terminal and storing the received portion of the biodata in a storage system, wherein the biodata being uploaded by the client terminal includes a plurality of sequences configured according to a specific format, where each of the plurality of sequences includes at least one row;

extracting at least one sequence from the received portion of the biodata, based on information on a sequence configuration rule of the specific format;

verifying whether each of the extracted at least one sequence is valid by analyzing information in rows of each of the extracted at least one sequence;

calculating a sequence error ratio when an erroneous sequence is discovered as a result of the verifying step; and

suspending an upload of a remaining portion of the biodata when the calculated sequence error ratio exceeds a threshold value,

wherein the verifying step includes;

verifying whether rows of a target sequence to be currently verified among the extracted at least one sequence satisfy a row verification condition defined based on the sequence configuration rule of the specific format;

determining the target sequence as the erroneous sequence when at least one of the rows of the target sequence does not satisfy the row verification condition; and

determining the target sequence as a valid sequence when the rows of the target sequence satisfy the row verification condition; and

wherein the calculating step includes;

calculating a ratio of a number of erroneous sequences to an estimated total number of sequences of the biodata when the target sequence is determined as the erroneous sequence, wherein the erroneous sequences include previously-determined erroneous sequences and the target sequence currently determined as the erroneous sequence.

2. The method according to claim 1, wherein the verifying whether the rows of the target sequence satisfy the row verification condition comprises:

verifying whether a first row of the target sequence starts with a character ‘

@’

; and

verifying whether a valid character is recorded on a second row of the target sequence.

3. The method according to claim 2, wherein the verifying whether the rows of the target sequence satisfy the row verification condition further comprises:

verifying whether a character ‘

+’

is recorded on a third row of the target sequence;

verifying whether a character belonging in a preset American Standard Code for Information Interchange (ASCII) range is recorded on a fourth row of the target sequence; and

verifying whether a number of characters on the second row is equal to a number of characters on the fourth row.

4. The method according to claim 2, wherein the valid character comprises at least one of ‘

A’

, ‘

T’

, ‘

G’

, ‘

C’

, and ‘

N’

.

5. The method according to claim 1, wherein the verifying step comprises:

when the target sequence is determined as the erroneous sequence, recording identification information of the target sequence in an error list and storing the error list in the storage system.

6. The method according to claim 1, after the suspending step, the method further comprises:

notifying an occurrence of an error in the biodata to the client terminal; and

deleting portions of the biodata stored in the storage system.

7. The method according to claim 1, wherein the verifying step comprises:

decompressing the received portion of the biodata in real time.

8. The method according to claim 1, wherein the calculating step comprises:

identifying a total amount of the biodata;

estimating a total number of sequences recorded in the entire biodata based on the total amount; and

calculating the sequence error ratio by dividing the number of the erroneous sequences with the estimated total number of sequences.

9. The method according to claim 1, wherein the specific format includes a FASTQ format.

10. The method according to claim 8, wherein the total amount of the biodata is identified from file information included in a header of a first received portion of the biodata.