WO2014037914A3 - Method and system for organizing and retrieving data in a semantic database structure - Google Patents

Method and system for organizing and retrieving data in a semantic database structure Download PDF

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Publication number
WO2014037914A3
WO2014037914A3 PCT/IB2013/058349 IB2013058349W WO2014037914A3 WO 2014037914 A3 WO2014037914 A3 WO 2014037914A3 IB 2013058349 W IB2013058349 W IB 2013058349W WO 2014037914 A3 WO2014037914 A3 WO 2014037914A3
Authority
WO
WIPO (PCT)
Prior art keywords
semantic
data
disease
organizing
edges
Prior art date
Application number
PCT/IB2013/058349
Other languages
French (fr)
Other versions
WO2014037914A2 (en
Inventor
Junaid GAMIELDIEN
Original Assignee
University Of The Western Cape
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 University Of The Western Cape filed Critical University Of The Western Cape
Publication of WO2014037914A2 publication Critical patent/WO2014037914A2/en
Publication of WO2014037914A3 publication Critical patent/WO2014037914A3/en

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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
    • 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
    • G16B5/00—ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic 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
    • 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
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations

Landscapes

  • Physics & Mathematics (AREA)
  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Theoretical Computer Science (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Evolutionary Biology (AREA)
  • General Health & Medical Sciences (AREA)
  • Medical Informatics (AREA)
  • Molecular Biology (AREA)
  • Databases & Information Systems (AREA)
  • Bioethics (AREA)
  • Analytical Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Genetics & Genomics (AREA)
  • Chemical & Material Sciences (AREA)
  • Physiology (AREA)
  • Information Retrieval, Db Structures And Fs Structures Therefor (AREA)

Abstract

A method and system for managing information relating to bio-ontological data are disclosed. The method includes defining a semantic network representing bio-ontologicai data, and storing the data as a directed acyclic graph (DAG) having nodes and edges, wherein the nodes represent concepts that can have any number of attributes and the edges are directed and represent semantic relationships between concepts. The semantic network is defined by a semantic model which enforces the allowable relationships between a plurality of concept classes in a core database. The semantic model includes cross-ontology mapping of phenotypes, pathways and functions known to be associated with a disease of interest, resulting in a meta-ontology in which genes are transitively associated with a disease.
PCT/IB2013/058349 2012-09-07 2013-09-06 Method and system for organizing and retrieving data in a semantic database structure WO2014037914A2 (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
ZA2012/06733 2012-09-07
ZA201206733 2012-09-07

Publications (2)

Publication Number Publication Date
WO2014037914A2 WO2014037914A2 (en) 2014-03-13
WO2014037914A3 true WO2014037914A3 (en) 2014-05-30

Family

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Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/IB2013/058349 WO2014037914A2 (en) 2012-09-07 2013-09-06 Method and system for organizing and retrieving data in a semantic database structure

Country Status (1)

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WO (1) WO2014037914A2 (en)

Families Citing this family (8)

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CN109643578B (en) * 2016-06-01 2023-07-21 生命科技股份有限公司 Methods and systems for designing gene combinations
US10372883B2 (en) 2016-06-24 2019-08-06 Scripps Networks Interactive, Inc. Satellite and central asset registry systems and methods and rights management systems
US10452714B2 (en) 2016-06-24 2019-10-22 Scripps Networks Interactive, Inc. Central asset registry system and method
US11868445B2 (en) 2016-06-24 2024-01-09 Discovery Communications, Llc Systems and methods for federated searches of assets in disparate dam repositories
US11200279B2 (en) 2017-04-17 2021-12-14 Datumtron Corp. Datumtronic knowledge server
US10657179B2 (en) * 2017-09-01 2020-05-19 X Development Llc Bipartite graph structure
GB201805074D0 (en) * 2018-03-28 2018-05-09 Benevolental Tech Limited Search Tool For Knowledge Discovery
CN111859969B (en) * 2020-07-20 2024-05-03 航天科工智慧产业发展有限公司 Data analysis method and device, electronic equipment and storage medium

Citations (6)

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CA2306579A1 (en) * 2000-04-21 2001-10-21 Malibu Engineering & Software Ltd. Document-based database management system and method
US20060178862A1 (en) * 2001-01-19 2006-08-10 Chan John W Methods and systems for designing machines including biologically-derived parts
US20080027929A1 (en) * 2006-07-12 2008-01-31 International Business Machines Corporation Computer-based method for finding similar objects using a taxonomy
US20100070448A1 (en) * 2002-06-24 2010-03-18 Nosa Omoigui System and method for knowledge retrieval, management, delivery and presentation
US20110047148A1 (en) * 2006-07-27 2011-02-24 Nosa Omoigui Information nervous system
US20110119221A1 (en) * 2005-06-20 2011-05-19 New York University Method, system and software arrangement for reconstructing formal descriptive models of processes from functional/modal data using suitable ontology

Patent Citations (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CA2306579A1 (en) * 2000-04-21 2001-10-21 Malibu Engineering & Software Ltd. Document-based database management system and method
US20060178862A1 (en) * 2001-01-19 2006-08-10 Chan John W Methods and systems for designing machines including biologically-derived parts
US20100070448A1 (en) * 2002-06-24 2010-03-18 Nosa Omoigui System and method for knowledge retrieval, management, delivery and presentation
US20110119221A1 (en) * 2005-06-20 2011-05-19 New York University Method, system and software arrangement for reconstructing formal descriptive models of processes from functional/modal data using suitable ontology
US20080027929A1 (en) * 2006-07-12 2008-01-31 International Business Machines Corporation Computer-based method for finding similar objects using a taxonomy
US20110047148A1 (en) * 2006-07-27 2011-02-24 Nosa Omoigui Information nervous system

Non-Patent Citations (2)

* Cited by examiner, † Cited by third party
Title
CHEN ET AL.: "Semantic web for integrated network analysis in biomedicine.", 6 January 2009 (2009-01-06), Retrieved from the Internet <URL:http://www.lexgrid.org/LCD/images/3135/SemanticWeb-NetworkAnalysis-Medicine.pdf> [retrieved on 20140304] *
DINATALE.: "A Heuristic Ontological Model of Protein Complexes A Case Study Based on the E3 Ubiquitin Ligase Protein Complexes of Arabidopsis thaliana.", 1 January 2012 (2012-01-01), Retrieved from the Internet <URL:http://scholar.uwindsor.ca/cgi/viewcontent.cgi?article=5799&context=etd&sei-redir=1&referer=http%3A%2F%2Fscholar.google.com%2Fscholar%3Fq%3Dmanage%2Binformation%2Bbio-ontological%2Bdata%2Bsemantic%2Bnetwork%2Bdirected%2Bacyclic%2Bgraph%2B%2528DAG%2529%2B%26btnG%3D%26h1%3Den%26assdt%3D1%252C5> [retrieved on 20140304] *

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