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

Info

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

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
    • 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

ID=50237720

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)

Country Link
WO (1) WO2014037914A2 (en)

Families Citing this family (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2017210437A1 (en) * 2016-06-01 2017-12-07 Life Technologies Corporation Methods and systems for designing gene panels
US11868445B2 (en) 2016-06-24 2024-01-09 Discovery Communications, Llc Systems and methods for federated searches of assets in disparate dam repositories
US10452714B2 (en) 2016-06-24 2019-10-22 Scripps Networks Interactive, Inc. Central asset registry system and method
US10372883B2 (en) 2016-06-24 2019-08-06 Scripps Networks Interactive, Inc. Satellite and central asset registry systems and methods and rights management systems
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)

* 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
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.***.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] *

Also Published As

Publication number Publication date
WO2014037914A2 (en) 2014-03-13

Similar Documents

Publication Publication Date Title
WO2014037914A3 (en) Method and system for organizing and retrieving data in a semantic database structure
WO2014140908A3 (en) Systems and methods for handling user editing history
WO2012039760A8 (en) Processing of categorized product information
IN2015DN00097A (en)
WO2012106677A3 (en) Method and system for image analysis and interpretation
WO2009134755A3 (en) Adaptive knowledge platform
Fernández Pérez et al. The endurance of family businesses. A global overview
WO2013177508A3 (en) Enterprise-scalable model-based analytics
WO2013074480A3 (en) Method and system for selection of patients to receive a medical device
WO2013188010A3 (en) System and method of designing models in a feedback loop
WO2012135164A3 (en) Cable management and inventory enhancement
WO2014022901A3 (en) Method and system implemented by a collaborative distributed computational network, and related devices
WO2013150234A3 (en) Method and device for processing information
MX368512B (en) Dynamically scalable distributed heterogenous platform relational database.
WO2009141802A3 (en) Management infon, method and system for workflow management in a communications network
Arrigo Luxury brands enter the online market
EP2565791A4 (en) Storage system, control method for storage system, and computer program
Carloni The paradoxical Relationship between Arts and Management: Corporate Collection's for Organization's Value Creation
Cennamo et al. Caring about firm stakeholders: Towards a theory of proactive stakeholder management
Girola Startups' business model in an innovative industry: the case of drones
Gallo et al. Simulation model to analyze transport, handling, temporary storage and sorting issues: a valuable way to support layout, system definition and configuration and scheduling decision
MARINO Blue ocean strategy: a literature review and a framework for future research agenda
Pinna Embeddedness Of Organic Producers Enrolled In AFNs: A Comparison Between Two European Regions.
Michetti PaaST: Preservation as a Service for Trust
DI MAURO Morte dell'imprenditore e fallimento (artt. 11, 12, 18, 20, RD 16.3. 1942, n. 267).

Legal Events

Date Code Title Description
121 Ep: the epo has been informed by wipo that ep was designated in this application

Ref document number: 13835426

Country of ref document: EP

Kind code of ref document: A2

122 Ep: pct application non-entry in european phase

Ref document number: 13835426

Country of ref document: EP

Kind code of ref document: A2