SG11201903180RA - Method and system for storing and accessing bioinformatics data - Google Patents

Method and system for storing and accessing bioinformatics data

Info

Publication number
SG11201903180RA
SG11201903180RA SG11201903180RA SG11201903180RA SG11201903180RA SG 11201903180R A SG11201903180R A SG 11201903180RA SG 11201903180R A SG11201903180R A SG 11201903180RA SG 11201903180R A SG11201903180R A SG 11201903180RA SG 11201903180R A SG11201903180R A SG 11201903180RA
Authority
SG
Singapore
Prior art keywords
international
ptr
class
data
accessing
Prior art date
Application number
SG11201903180RA
Inventor
Daniele Renzi
Giorgio Zoia
Original Assignee
Genomsys Sa
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Genomsys Sa filed Critical Genomsys Sa
Publication of SG11201903180RA publication Critical patent/SG11201903180RA/en

Links

Classifications

    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B50/00—ICT programming tools or database systems specially adapted for bioinformatics
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B50/00—ICT programming tools or database systems specially adapted for bioinformatics
    • G16B50/30—Data warehousing; Computing architectures
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F17/00—Digital computing or data processing equipment or methods, specially adapted for specific functions
    • G06F17/10—Complex mathematical operations
    • G06F17/16—Matrix or vector computation, e.g. matrix-matrix or matrix-vector multiplication, matrix factorization
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F17/00—Digital computing or data processing equipment or methods, specially adapted for specific functions
    • G06F17/10—Complex mathematical operations
    • G06F17/18—Complex mathematical operations for evaluating statistical data, e.g. average values, frequency distributions, probability functions, regression analysis
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/10—Sequence alignment; Homology search
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • G16B40/10—Signal processing, e.g. from mass spectrometry [MS] or from PCR
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B50/00—ICT programming tools or database systems specially adapted for bioinformatics
    • G16B50/20—Heterogeneous data integration
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6869—Methods for sequencing
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids

Landscapes

  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Theoretical Computer Science (AREA)
  • Medical Informatics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Evolutionary Biology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Biotechnology (AREA)
  • General Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • Databases & Information Systems (AREA)
  • Data Mining & Analysis (AREA)
  • General Physics & Mathematics (AREA)
  • Bioethics (AREA)
  • Mathematical Physics (AREA)
  • Mathematical Optimization (AREA)
  • Mathematical Analysis (AREA)
  • Pure & Applied Mathematics (AREA)
  • Computational Mathematics (AREA)
  • Software Systems (AREA)
  • Chemical & Material Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • General Engineering & Computer Science (AREA)
  • Analytical Chemistry (AREA)
  • Algebra (AREA)
  • Artificial Intelligence (AREA)
  • Public Health (AREA)
  • Epidemiology (AREA)
  • Evolutionary Computation (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Molecular Biology (AREA)
  • Organic Chemistry (AREA)
  • Operations Research (AREA)
  • Probability & Statistics with Applications (AREA)
  • Signal Processing (AREA)
  • Computing Systems (AREA)
  • Wood Science & Technology (AREA)

Abstract

INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (43) International Publication Date 19 April 2018 (19.04.2018) WIP01 PCT onion °nolo imiolonomo oimIE (10) International Publication Number WO 2018/068828 Al (51) International Patent Classification: GO6F 19/28 (2011.01) G06F 19/22 (2011.01) (21) International Application Number: PCT/EP2016/074301 (22) International Filing Date: 11 October 2016 (11.10.2016) (25) Filing Language: English (26) Publication Language: English (71) Applicant: GENOMSYS SA [CH/CH]; Chemin de la Raye 13, 1024 Ecublens VD (CH). (72) Inventors: RENZI, Daniele; Route Aloys-Fauquez 105, 1018 Lausanne (CH). ZOIA, Giorgio; Chemin des Croix- Rouges 10, 1007 Lausanne (CH). (74) Agent: DE ANNA, Pier Luigi; Schubertstr. 10, 80336 Mfinchen (DE). (81) Designated States (unless otherwise indicated, for every kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (84) Designated States (unless otherwise indicated, for every kind of regional protection available): ARIPO (BW, GH, GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, KM, ML, MR, NE, SN, TD, TG). Published: with international search report (Art. 21(3)) (54) Title: METHOD AND SYSTEM FOR STORING AND ACCESSING BIOINFORMATICS DATA Type 1 2 3 ... N Class P ptr ..-_____, Class N ptr .p...-......„ .„ Class M ptr ---„i Class I ptr Metadata --] Metadata Access Units mapping positions Position on the reference sequence of the first read in each AU These pointers are used to \"jump\" to physical positions in the reference sequence Figure 21 - The Master Index Table contains the positions on the reference sequences of the first read in each AU. el (57) : Method and system for storing and accessing genomic data. Genomic sequencing data are partitioned into access units of different types based on the predictability of the contained data. Access units are classified in different types and the structuring t enables selective access and selective processing of genomic data.
SG11201903180RA 2016-10-11 2016-10-11 Method and system for storing and accessing bioinformatics data SG11201903180RA (en)

Applications Claiming Priority (1)

Application Number Priority Date Filing Date Title
PCT/EP2016/074301 WO2018068828A1 (en) 2016-10-11 2016-10-11 Method and system for storing and accessing bioinformatics data

Publications (1)

Publication Number Publication Date
SG11201903180RA true SG11201903180RA (en) 2019-05-30

Family

ID=57241049

Family Applications (1)

Application Number Title Priority Date Filing Date
SG11201903180RA SG11201903180RA (en) 2016-10-11 2016-10-11 Method and system for storing and accessing bioinformatics data

Country Status (16)

Country Link
US (1) US11386979B2 (en)
EP (1) EP3526710A1 (en)
JP (1) JP7092757B2 (en)
KR (1) KR20190073428A (en)
CN (1) CN110168652B (en)
AU (1) AU2016426570A1 (en)
BR (1) BR112019007307A2 (en)
CA (1) CA3039689A1 (en)
CL (1) CL2019000956A1 (en)
CO (1) CO2019003599A2 (en)
EA (1) EA037106B1 (en)
IL (1) IL265909B1 (en)
MX (1) MX2019004123A (en)
PH (1) PH12019500794A1 (en)
SG (1) SG11201903180RA (en)
WO (1) WO2018068828A1 (en)

Families Citing this family (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US11386979B2 (en) 2016-10-11 2022-07-12 Genomsys Sa Method and system for storing and accessing bioinformatics data
CN111028883B (en) * 2019-11-20 2023-07-18 广州达美智能科技有限公司 Gene processing method and device based on Boolean algebra and readable storage medium
EP3896698A1 (en) 2020-04-15 2021-10-20 Genomsys SA Method and system for the efficient data compression in mpeg-g
KR102418617B1 (en) * 2020-10-13 2022-07-07 서울대학교산학협력단 DNA storage encoding methods, programs and devices that limit base ratio and successive occurrences

Family Cites Families (10)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
JP2003188735A (en) 2001-12-13 2003-07-04 Ntt Data Corp Data compressing device and method, and program
US20040153255A1 (en) 2003-02-03 2004-08-05 Ahn Tae-Jin Apparatus and method for encoding DNA sequence, and computer readable medium
WO2006052242A1 (en) * 2004-11-08 2006-05-18 Seirad, Inc. Methods and systems for compressing and comparing genomic data
JP4852313B2 (en) 2006-01-20 2012-01-11 富士通株式会社 Genome analysis program, recording medium recording the program, genome analysis apparatus, and genome analysis method
US20100268520A1 (en) * 2007-08-02 2010-10-21 Carlos Llopis Llopis Electronic System to Emulate the Chain of the "DNA" Structure of a Chromosome
WO2012031029A2 (en) * 2010-08-31 2012-03-08 Lawrence Ganeshalingam Method and systems for processing polymeric sequence data and related information
WO2013067542A1 (en) * 2011-11-03 2013-05-10 Genformatic, Llc Device, system and method for securing and comparing genomic data
US9734284B2 (en) * 2013-03-15 2017-08-15 Micron Technology, Inc. Hardware acceleration of short read mapping for genomic and other types of analyses
US10902937B2 (en) 2014-02-12 2021-01-26 International Business Machines Corporation Lossless compression of DNA sequences
US11386979B2 (en) 2016-10-11 2022-07-12 Genomsys Sa Method and system for storing and accessing bioinformatics data

Also Published As

Publication number Publication date
BR112019007307A2 (en) 2019-09-17
WO2018068828A9 (en) 2019-09-12
US20200058378A1 (en) 2020-02-20
EA037106B1 (en) 2021-02-05
PH12019500794A1 (en) 2019-12-02
CO2019003599A2 (en) 2019-08-30
CN110168652B (en) 2023-11-21
JP2019537781A (en) 2019-12-26
AU2016426570A9 (en) 2019-10-03
CL2019000956A1 (en) 2019-08-23
EP3526710A1 (en) 2019-08-21
JP7092757B2 (en) 2022-06-28
AU2016426570A1 (en) 2019-06-06
IL265909A (en) 2019-06-30
EA201990920A1 (en) 2019-07-31
CN110168652A (en) 2019-08-23
IL265909B1 (en) 2024-03-01
US11386979B2 (en) 2022-07-12
CA3039689A1 (en) 2018-04-19
WO2018068828A1 (en) 2018-04-19
KR20190073428A (en) 2019-06-26
MX2019004123A (en) 2019-06-10

Similar Documents

Publication Publication Date Title
SG11201809963XA (en) Application framework using blockchain-based asset ownership
SG11201903271UA (en) Method and systems for the indexing of bioinformatics data
SG11201903137XA (en) Three-dimensional graphical user interface for informational input in virtual reality environment
SG11201807848PA (en) Efficient live-migration of remotely accessed data
SG11201904942YA (en) Blockchain-based service execution method and apparatus, and electronic device
SG11201407485RA (en) Compare and replace dat table entry
SG11201903180RA (en) Method and system for storing and accessing bioinformatics data
SG11201806653SA (en) Systems and methods for providing identity scores
SG11201809294RA (en) Systems and methods for sensor data analysis through machine learning
SG11201807334SA (en) Methods, compositions, and devices for information storage
SG11201907663XA (en) Method and device for constructing scoring model and evaluating user credit
SG11201805300QA (en) Heterocyclic compounds as immunomodulators
SG11201804190YA (en) Method and system for blockchain variant using digital signatures
SG11201805645QA (en) Lsd1 inhibitors
SG11201810611YA (en) Coumarin compounds and their uses as fluorescent labels
SG11201808598UA (en) Detecting microbial infection in wounds
SG11201901371XA (en) Methods for the detection of genomic copy changes in dna samples
SG11201903108UA (en) Order information determination method and apparatus
SG11201805906WA (en) Diagnostic and prognostic methods for cardiovascular diseases and events
SG11201804360XA (en) Mat2a inhibitors for treating mtap null cancer
SG11201806853VA (en) Abstracted graphs from social relationship graph
SG11201806825RA (en) A data source system agnostic fact category partitioned information repository and methods for the insertion and retrieval of data using the information repository
SG11201903548QA (en) User interface for informational input in virtual reality environment
SG11201811042PA (en) Payment information processing method, apparatus, and user device
SG11201903012RA (en) Anti-c1s antibodies and methods of use thereof