SG11201903174SA - Method and system for the transmission of bioinformatics data - Google Patents

Method and system for the transmission of bioinformatics data

Info

Publication number
SG11201903174SA
SG11201903174SA SG11201903174SA SG11201903174SA SG11201903174SA SG 11201903174S A SG11201903174S A SG 11201903174SA SG 11201903174S A SG11201903174S A SG 11201903174SA SG 11201903174S A SG11201903174S A SG 11201903174SA SG 11201903174S A SG11201903174S A SG 11201903174SA
Authority
SG
Singapore
Prior art keywords
gdmt
ridmt
international
genomic
header
Prior art date
Application number
SG11201903174SA
Inventor
Giorgio Zoia
Daniele Renzi
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 SG11201903174SA publication Critical patent/SG11201903174SA/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
    • G16B50/50—Compression of genetic data
    • G—PHYSICS
    • G08—SIGNALLING
    • G08C—TRANSMISSION SYSTEMS FOR MEASURED VALUES, CONTROL OR SIMILAR SIGNALS
    • G08C15/00—Arrangements characterised by the use of multiplexing for the transmission of a plurality of signals over a common path
    • 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
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/20—Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
    • 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
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • G16B25/10—Gene or protein expression profiling; Expression-ratio estimation or normalisation
    • 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
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/20—Sequence assembly
    • 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
    • G16B50/20—Heterogeneous data integration
    • 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

Abstract

INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property 1111110H 0 ill VIII N 3 E1 0 0111011011H M il HMO 11110 1111 OEN Organization International Bureau (10) International Publication Number . . .., . (43) International Publication Date WO 2018/068830 Al 19 April 2018 (19.04.2018) WIP0 I PCT (51) International Patent Classification: KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, GOOF 19/28 (2011.01) MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PA, (21) International Application Number: PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, SD, PCT/EP2016/074311 SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (22) International Filing Date: (84) Designated States (unless otherwise indicated, for every 11 October 2016 (11.10.2016) kind of regional protection available): ARIPO (BW, GH, (25) Filing Language: English GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, (26) Publication Language: English UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, (71) Applicant: GENOMSYS SA [CH/CH]; chemin de la Raye EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, 13, 1024 Ecublens VD (CH). 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, (72) Inventors: ZOIA, Giorgio; chemin des Croix-Rouges KM, ML, MR, NE, SN, TD, TG). 10, 1007 Lausanne (CH). RENZI, Daniele; route Aloys- Fauquez 105, 1018 Lausanne (CH). Published: (74) Agent: DE ANNA, Pier Luigi; Schubertstr. 10, 80336 — with international search report (Art. 21(3)) Miinchen (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, = (54) Title: METHOD AND SYSTEM FOR THE TRANSMISSION OF BIOINFORMATICS DATA = 2 81 One GDL stream per Multiplex = : GDL GDL 1 1 GDL = = GDMT GDMT GDMT i x-485One GDMT stream 480 483 — RIDMT RIDMT FRIDMT per Dataset t487 One RIDMT stream i per Dataset = ( t1 [Heade Packet i I I ].- Genomic = x n' to Headel i • B 1113c1 k[l 1 I streams = a) 0 1Heade 1 i U I 484 = _ .47+ ._ 486 M Access Units 5 2 c5 a, I L-leader i j 1 0 = Header . • ,- - C 482 • 0 c GDMT GDMT L GDMT t — (-9 13 I ea RIDMT RIDMT RIDMT ' 1-1 in Header ;packet cc Header : B o . I': 0 en C c.) Header . Ot Ot © ....... 11 © (57) : Method and system for ei multiplexing of a structured compressed 488 _,,, 486 /Access Units 489 4810 Figure 48 - Data encapsulation in a Genomic Multiplex. the transmission of genomic data. The transmission of genomic data is realized by employing the genomic dataset in a stream of genomic data partitioned into randomly accessible access units.
SG11201903174SA 2016-10-11 2016-10-11 Method and system for the transmission of bioinformatics data SG11201903174SA (en)

Applications Claiming Priority (1)

Application Number Priority Date Filing Date Title
PCT/EP2016/074311 WO2018068830A1 (en) 2016-10-11 2016-10-11 Method and system for the transmission of bioinformatics data

Publications (1)

Publication Number Publication Date
SG11201903174SA true SG11201903174SA (en) 2019-05-30

Family

ID=57241051

Family Applications (1)

Application Number Title Priority Date Filing Date
SG11201903174SA SG11201903174SA (en) 2016-10-11 2016-10-11 Method and system for the transmission of bioinformatics data

Country Status (19)

Country Link
US (1) US20200051668A1 (en)
EP (1) EP3526712B1 (en)
JP (1) JP6949970B2 (en)
KR (1) KR20190062543A (en)
CN (1) CN110178183B (en)
AU (1) AU2016426572A1 (en)
BR (1) BR112019007313A2 (en)
CA (1) CA3039692A1 (en)
CL (1) CL2019000955A1 (en)
CO (1) CO2019003580A2 (en)
EA (1) EA201990931A1 (en)
ES (1) ES2867874T3 (en)
IL (1) IL265907A (en)
MX (1) MX2019004126A (en)
PE (1) PE20191059A1 (en)
PH (1) PH12019500795A1 (en)
PL (1) PL3526712T3 (en)
SG (1) SG11201903174SA (en)
WO (1) WO2018068830A1 (en)

Families Citing this family (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US10554220B1 (en) 2019-01-30 2020-02-04 International Business Machines Corporation Managing compression and storage of genomic data
WO2020231590A1 (en) * 2019-05-14 2020-11-19 Blayne Lequeux Healthcare data cloud system, server and method
EP3896698A1 (en) 2020-04-15 2021-10-20 Genomsys SA Method and system for the efficient data compression in mpeg-g

Family Cites Families (16)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
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
KR101819180B1 (en) * 2010-03-31 2018-01-16 한국전자통신연구원 Encoding method and apparatus, and deconding method and apparatus
EP2544113A1 (en) * 2011-07-05 2013-01-09 Koninklijke Philips Electronics N.V. Genomic/proteomic sequence representation, visualization, comparison and reporting using a bioinformatics character set and a mapped bioinformatics font
KR101922129B1 (en) * 2011-12-05 2018-11-26 삼성전자주식회사 Method and apparatus for compressing and decompressing genetic information using next generation sequencing(NGS)
WO2013086355A1 (en) * 2011-12-08 2013-06-13 Five3 Genomics, Llc Distributed system providing dynamic indexing and visualization of genomic data
US20140108323A1 (en) * 2012-10-12 2014-04-17 Bonnie Berger Leighton Compressively-accelerated read mapping
GB202020510D0 (en) * 2013-01-17 2021-02-03 Edico Genome Corp Bioinformatics systems, apparatuses, and methods executed on an integrated circuit processing platform
CN103971694B (en) * 2013-01-29 2016-12-28 华为技术有限公司 The Forecasting Methodology of bandwidth expansion band signal, decoding device
CN103336916B (en) * 2013-07-05 2016-04-06 中国科学院数学与系统科学研究院 A kind of sequencing sequence mapping method and system
NL2012222C2 (en) * 2014-02-06 2015-08-10 Genalice B V A method of storing/reconstructing a multitude of sequences in/from a data storage structure.
US10902937B2 (en) * 2014-02-12 2021-01-26 International Business Machines Corporation Lossless compression of DNA sequences
US10116632B2 (en) * 2014-09-12 2018-10-30 New York University System, method and computer-accessible medium for secure and compressed transmission of genomic data
US11789906B2 (en) * 2014-11-19 2023-10-17 Arc Bio, Llc Systems and methods for genomic manipulations and analysis
CN107004068B (en) * 2014-11-25 2021-08-24 皇家飞利浦有限公司 Secure transmission of genomic data
US10394763B2 (en) * 2015-05-19 2019-08-27 Samsung Electronics Co., Ltd. Method and device for generating pileup file from compressed genomic data
US11393559B2 (en) * 2016-03-09 2022-07-19 Sophia Genetics S.A. Methods to compress, encrypt and retrieve genomic alignment data

Also Published As

Publication number Publication date
CN110178183B (en) 2023-11-21
BR112019007313A2 (en) 2019-09-17
US20200051668A1 (en) 2020-02-13
CN110178183A (en) 2019-08-27
PL3526712T3 (en) 2021-12-13
CA3039692A1 (en) 2018-04-19
PE20191059A1 (en) 2019-08-06
IL265907A (en) 2019-06-30
WO2018068830A9 (en) 2018-08-30
PH12019500795A1 (en) 2019-12-02
WO2018068830A1 (en) 2018-04-19
EP3526712A1 (en) 2019-08-21
CL2019000955A1 (en) 2019-08-23
ES2867874T3 (en) 2021-10-21
EA201990931A1 (en) 2019-11-29
MX2019004126A (en) 2019-06-12
EP3526712B1 (en) 2021-03-24
CO2019003580A2 (en) 2019-08-30
JP2019537170A (en) 2019-12-19
JP6949970B2 (en) 2021-10-13
KR20190062543A (en) 2019-06-05
AU2016426572A1 (en) 2019-06-06

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