BR112019007363A2 - método e aparelho para o acesso aos dados bioinformáticos estruturados nas unidades de acesso - Google Patents

método e aparelho para o acesso aos dados bioinformáticos estruturados nas unidades de acesso

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Publication number
BR112019007363A2
BR112019007363A2 BR112019007363A BR112019007363A BR112019007363A2 BR 112019007363 A2 BR112019007363 A2 BR 112019007363A2 BR 112019007363 A BR112019007363 A BR 112019007363A BR 112019007363 A BR112019007363 A BR 112019007363A BR 112019007363 A2 BR112019007363 A2 BR 112019007363A2
Authority
BR
Brazil
Prior art keywords
access
genomic
coding
descriptor sets
data
Prior art date
Application number
BR112019007363A
Other languages
English (en)
Inventor
Alberti Claudio
Renzi Daniele
Zoia Giorgio
Khoso Baluch Mohamed
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
Priority claimed from PCT/EP2016/074307 external-priority patent/WO2018068829A1/en
Priority claimed from PCT/EP2016/074311 external-priority patent/WO2018068830A1/en
Priority claimed from PCT/EP2016/074301 external-priority patent/WO2018068828A1/en
Priority claimed from PCT/EP2016/074297 external-priority patent/WO2018068827A1/en
Application filed by Genomsys Sa filed Critical Genomsys Sa
Priority claimed from PCT/US2017/041579 external-priority patent/WO2018071078A1/en
Publication of BR112019007363A2 publication Critical patent/BR112019007363A2/pt

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Classifications

    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F16/00—Information retrieval; Database structures therefor; File system structures therefor
    • G06F16/20—Information retrieval; Database structures therefor; File system structures therefor of structured data, e.g. relational data
    • G06F16/22—Indexing; Data structures therefor; Storage structures
    • G06F16/2282—Tablespace storage structures; Management thereof
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F16/00—Information retrieval; Database structures therefor; File system structures therefor
    • G06F16/20—Information retrieval; Database structures therefor; File system structures therefor of structured data, e.g. relational data
    • G06F16/23—Updating
    • G06F16/2365—Ensuring data consistency and integrity
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F16/00—Information retrieval; Database structures therefor; File system structures therefor
    • G06F16/20—Information retrieval; Database structures therefor; File system structures therefor of structured data, e.g. relational data
    • G06F16/28—Databases characterised by their database models, e.g. relational or object models
    • G06F16/284—Relational databases
    • G06F16/285—Clustering or classification
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F21/00—Security arrangements for protecting computers, components thereof, programs or data against unauthorised activity
    • G06F21/60—Protecting data
    • G06F21/602—Providing cryptographic facilities or services
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F21/00—Security arrangements for protecting computers, components thereof, programs or data against unauthorised activity
    • G06F21/60—Protecting data
    • G06F21/62—Protecting access to data via a platform, e.g. using keys or access control rules
    • G06F21/6218—Protecting access to data via a platform, e.g. using keys or access control rules to a system of files or objects, e.g. local or distributed file system or database
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F21/00—Security arrangements for protecting computers, components thereof, programs or data against unauthorised activity
    • G06F21/60—Protecting data
    • G06F21/62—Protecting access to data via a platform, e.g. using keys or access control rules
    • G06F21/6218—Protecting access to data via a platform, e.g. using keys or access control rules to a system of files or objects, e.g. local or distributed file system or database
    • G06F21/6245—Protecting personal data, e.g. for financial or medical purposes
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F3/00—Input arrangements for transferring data to be processed into a form capable of being handled by the computer; Output arrangements for transferring data from processing unit to output unit, e.g. interface arrangements
    • G06F3/01—Input arrangements or combined input and output arrangements for interaction between user and computer
    • G06F3/048—Interaction techniques based on graphical user interfaces [GUI]
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F7/00—Methods or arrangements for processing data by operating upon the order or content of the data handled
    • 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
    • G16B20/10—Ploidy or copy number 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
    • 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
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • 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
    • 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
    • G16B45/00—ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks
    • 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
    • G16B50/10—Ontologies; Annotations
    • 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
    • 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
    • G16B50/40—Encryption of genetic data
    • 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
    • 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
    • G16B99/00—Subject matter not provided for in other groups of this subclass
    • H—ELECTRICITY
    • H03—ELECTRONIC CIRCUITRY
    • H03M—CODING; DECODING; CODE CONVERSION IN GENERAL
    • H03M7/00—Conversion of a code where information is represented by a given sequence or number of digits to a code where the same, similar or subset of information is represented by a different sequence or number of digits
    • H03M7/30—Compression; Expansion; Suppression of unnecessary data, e.g. redundancy reduction
    • H03M7/3084—Compression; Expansion; Suppression of unnecessary data, e.g. redundancy reduction using adaptive string matching, e.g. the Lempel-Ziv method
    • H03M7/3086—Compression; Expansion; Suppression of unnecessary data, e.g. redundancy reduction using adaptive string matching, e.g. the Lempel-Ziv method employing a sliding window, e.g. LZ77
    • H—ELECTRICITY
    • H03—ELECTRONIC CIRCUITRY
    • H03M—CODING; DECODING; CODE CONVERSION IN GENERAL
    • H03M7/00—Conversion of a code where information is represented by a given sequence or number of digits to a code where the same, similar or subset of information is represented by a different sequence or number of digits
    • H03M7/30—Compression; Expansion; Suppression of unnecessary data, e.g. redundancy reduction
    • H03M7/70—Type of the data to be coded, other than image and sound

Landscapes

  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Theoretical Computer Science (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • General Health & Medical Sciences (AREA)
  • Medical Informatics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Biotechnology (AREA)
  • Evolutionary Biology (AREA)
  • Biophysics (AREA)
  • Databases & Information Systems (AREA)
  • Bioethics (AREA)
  • General Engineering & Computer Science (AREA)
  • General Physics & Mathematics (AREA)
  • Analytical Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Chemical & Material Sciences (AREA)
  • Data Mining & Analysis (AREA)
  • Software Systems (AREA)
  • Genetics & Genomics (AREA)
  • Molecular Biology (AREA)
  • Computer Security & Cryptography (AREA)
  • Computer Hardware Design (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Public Health (AREA)
  • Evolutionary Computation (AREA)
  • Epidemiology (AREA)
  • Artificial Intelligence (AREA)
  • Human Computer Interaction (AREA)
  • Signal Processing (AREA)
  • Management, Administration, Business Operations System, And Electronic Commerce (AREA)
  • Information Retrieval, Db Structures And Fs Structures Therefor (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Compression, Expansion, Code Conversion, And Decoders (AREA)
  • Detection And Prevention Of Errors In Transmission (AREA)
  • Labeling Devices (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)

Abstract

método e aparelho para codificação e acesso seletivo de dados de sequência genômica comprimida produzidos por máquinas de seqüenciamento genômico. o processo de codificação baseia-se no alinhamento de leituras de sequências em relação a sequências de referência preexistentes ou construções, na classificação e codificação das leituras de sequências por meio de conjuntos de descritores e particionamento adicional dos conjuntos de descritores em unidades de acesso de diferentes tipos. o acesso seletivo eficiente a regiões genômicas específicas com a garantia de recuperar todas as leituras de sequência mapeadas para essas regiões é fornecido por: sinalizar o tipo de configuração de mapeamento de dados usado para armazenar ou transmitir os conjuntos de descritores, determinar o número mínimo de unidades de acesso que precisam ser recuperadas e decodificadoas para acessar uma região genômica, fornecendo uma tabela de índice principal que contém todas as informações para otimizar o processo de acesso de dados.
BR112019007363A 2016-10-11 2017-07-11 método e aparelho para o acesso aos dados bioinformáticos estruturados nas unidades de acesso BR112019007363A2 (pt)

Applications Claiming Priority (7)

Application Number Priority Date Filing Date Title
PCT/EP2016/074307 WO2018068829A1 (en) 2016-10-11 2016-10-11 Method and apparatus for compact representation of bioinformatics data
PCT/EP2016/074311 WO2018068830A1 (en) 2016-10-11 2016-10-11 Method and system for the transmission of bioinformatics data
PCT/EP2016/074301 WO2018068828A1 (en) 2016-10-11 2016-10-11 Method and system for storing and accessing bioinformatics data
PCT/EP2016/074297 WO2018068827A1 (en) 2016-10-11 2016-10-11 Efficient data structures for bioinformatics information representation
PCT/US2017/017842 WO2018071055A1 (en) 2016-10-11 2017-02-14 Method and apparatus for the compact representation of bioinformatics data
PCT/US2017/017841 WO2018071054A1 (en) 2016-10-11 2017-02-14 Method and system for selective access of stored or transmitted bioinformatics data
PCT/US2017/041579 WO2018071078A1 (en) 2016-10-11 2017-07-11 Method and apparatus for the access to bioinformatics data structured in access units

Publications (1)

Publication Number Publication Date
BR112019007363A2 true BR112019007363A2 (pt) 2019-07-09

Family

ID=61905752

Family Applications (7)

Application Number Title Priority Date Filing Date
BR112019007359A BR112019007359A2 (pt) 2016-10-11 2017-02-14 método e sistema para acesso seletivo dos dados bioinformáticos armazenados ou transmitidos
BR112019007357A BR112019007357A2 (pt) 2016-10-11 2017-07-11 método e sistemas para a indexação de dados de bioinformática
BR112019007363A BR112019007363A2 (pt) 2016-10-11 2017-07-11 método e aparelho para o acesso aos dados bioinformáticos estruturados nas unidades de acesso
BR112019007360A BR112019007360A2 (pt) 2016-10-11 2017-07-11 método e sistemas para a representação e processamento de dados de bioinformática utilizando sequências de referência
BR112019016230A BR112019016230A2 (pt) 2016-10-11 2017-12-14 método e sistemas para a reconstrução de sequências de referência genômicas a partir de leituras de sequência genômica comprimidas
BR112019016232A BR112019016232A2 (pt) 2016-10-11 2017-12-15 método e sistemas para a compressão eficiente de leituras de sequencia genômica
BR112019016236A BR112019016236A2 (pt) 2016-10-11 2018-02-14 método e aparelho para a representação compacta de dados de bioinformática usando descritores genômicos múltiplos referência cruzada a pedidos relacionados

Family Applications Before (2)

Application Number Title Priority Date Filing Date
BR112019007359A BR112019007359A2 (pt) 2016-10-11 2017-02-14 método e sistema para acesso seletivo dos dados bioinformáticos armazenados ou transmitidos
BR112019007357A BR112019007357A2 (pt) 2016-10-11 2017-07-11 método e sistemas para a indexação de dados de bioinformática

Family Applications After (4)

Application Number Title Priority Date Filing Date
BR112019007360A BR112019007360A2 (pt) 2016-10-11 2017-07-11 método e sistemas para a representação e processamento de dados de bioinformática utilizando sequências de referência
BR112019016230A BR112019016230A2 (pt) 2016-10-11 2017-12-14 método e sistemas para a reconstrução de sequências de referência genômicas a partir de leituras de sequência genômica comprimidas
BR112019016232A BR112019016232A2 (pt) 2016-10-11 2017-12-15 método e sistemas para a compressão eficiente de leituras de sequencia genômica
BR112019016236A BR112019016236A2 (pt) 2016-10-11 2018-02-14 método e aparelho para a representação compacta de dados de bioinformática usando descritores genômicos múltiplos referência cruzada a pedidos relacionados

Country Status (17)

Country Link
US (6) US20200042735A1 (pt)
EP (3) EP3526694A4 (pt)
JP (4) JP2020505702A (pt)
KR (4) KR20190073426A (pt)
CN (6) CN110168651A (pt)
AU (3) AU2017342688A1 (pt)
BR (7) BR112019007359A2 (pt)
CA (3) CA3040138A1 (pt)
CL (6) CL2019000972A1 (pt)
CO (6) CO2019003595A2 (pt)
EA (2) EA201990917A1 (pt)
IL (3) IL265879B2 (pt)
MX (2) MX2019004130A (pt)
PE (7) PE20191058A1 (pt)
PH (6) PH12019550058A1 (pt)
SG (3) SG11201903270RA (pt)
WO (4) WO2018071054A1 (pt)

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CN113643761B (zh) * 2021-10-13 2022-01-18 苏州赛美科基因科技有限公司 一种用于解读二代测序结果所需数据的提取方法
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