WO2005036369A3 - Database for microbial investigations - Google Patents

Database for microbial investigations Download PDF

Info

Publication number
WO2005036369A3
WO2005036369A3 PCT/US2004/033742 US2004033742W WO2005036369A3 WO 2005036369 A3 WO2005036369 A3 WO 2005036369A3 US 2004033742 W US2004033742 W US 2004033742W WO 2005036369 A3 WO2005036369 A3 WO 2005036369A3
Authority
WO
WIPO (PCT)
Prior art keywords
pathogens
diseases
symptoms
information
database
Prior art date
Application number
PCT/US2004/033742
Other languages
French (fr)
Other versions
WO2005036369A2 (en
Inventor
Kumar Hari
John Mcneil
Dave Ecker
Neill White
Vivek Samant
Vanessa Zapp
Alan Goates
Original Assignee
Isis Pharmaceuticals Inc
Kumar Hari
John Mcneil
Dave Ecker
Neill White
Vivek Samant
Vanessa Zapp
Alan Goates
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 Isis Pharmaceuticals Inc, Kumar Hari, John Mcneil, Dave Ecker, Neill White, Vivek Samant, Vanessa Zapp, Alan Goates filed Critical Isis Pharmaceuticals Inc
Publication of WO2005036369A2 publication Critical patent/WO2005036369A2/en
Publication of WO2005036369A3 publication Critical patent/WO2005036369A3/en

Links

Classifications

    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16H—HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
    • G16H50/00—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics
    • G16H50/70—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for mining of medical data, e.g. analysing previous cases of other patients
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16H—HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
    • G16H50/00—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics
    • G16H50/80—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for detecting, monitoring or modelling epidemics or pandemics, e.g. flu
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16H—HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
    • G16H70/00—ICT specially adapted for the handling or processing of medical references
    • G16H70/60—ICT specially adapted for the handling or processing of medical references relating to pathologies
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A90/00—Technologies having an indirect contribution to adaptation to climate change
    • Y02A90/10—Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation

Landscapes

  • Engineering & Computer Science (AREA)
  • Public Health (AREA)
  • Health & Medical Sciences (AREA)
  • Medical Informatics (AREA)
  • General Health & Medical Sciences (AREA)
  • Primary Health Care (AREA)
  • Epidemiology (AREA)
  • Data Mining & Analysis (AREA)
  • Biomedical Technology (AREA)
  • Databases & Information Systems (AREA)
  • Pathology (AREA)
  • Information Retrieval, Db Structures And Fs Structures Therefor (AREA)
  • Management, Administration, Business Operations System, And Electronic Commerce (AREA)

Abstract

A centralized system provides for locating, storing and providing microbial-related information, including pathogens, diseases, symptoms, genetic information, and related documentation. A centralized database relates pathogens to diseases that they cause, symptoms of those diseases, genetic information about the pathogens, and documentation that is associated with any of the above. By analyzing the stored data, the system recognizes duplicated information, for example a pathogen present in the database twice, each time under a different taxonomical name, and creates a link from one instance of the pathogen to the other. The system additionally identifies common genes and sequences among related organisms. A researcher uses the system to perform investigations. For example, a medical doctor can enter patient symptoms to obtain a list of consistent diseases and associated pathogens. The system also tracks the progression of an outbreak and identifies similar occurrences by searching the World Wide Web and reporting results.
PCT/US2004/033742 2003-10-09 2004-10-12 Database for microbial investigations WO2005036369A2 (en)

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
US50991103P 2003-10-09 2003-10-09
US60/509,911 2003-10-09
US59840804P 2004-08-02 2004-08-02
US60/598,408 2004-08-02

Publications (2)

Publication Number Publication Date
WO2005036369A2 WO2005036369A2 (en) 2005-04-21
WO2005036369A3 true WO2005036369A3 (en) 2006-07-06

Family

ID=34437312

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2004/033742 WO2005036369A2 (en) 2003-10-09 2004-10-12 Database for microbial investigations

Country Status (1)

Country Link
WO (1) WO2005036369A2 (en)

Families Citing this family (42)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US7226739B2 (en) 2001-03-02 2007-06-05 Isis Pharmaceuticals, Inc Methods for rapid detection and identification of bioagents in epidemiological and forensic investigations
US20030027135A1 (en) 2001-03-02 2003-02-06 Ecker David J. Method for rapid detection and identification of bioagents
US7666588B2 (en) 2001-03-02 2010-02-23 Ibis Biosciences, Inc. Methods for rapid forensic analysis of mitochondrial DNA and characterization of mitochondrial DNA heteroplasmy
US20040121313A1 (en) 2002-12-06 2004-06-24 Ecker David J. Methods for rapid detection and identification of bioagents in organs for transplantation
US7217510B2 (en) 2001-06-26 2007-05-15 Isis Pharmaceuticals, Inc. Methods for providing bacterial bioagent characterizing information
US8073627B2 (en) 2001-06-26 2011-12-06 Ibis Biosciences, Inc. System for indentification of pathogens
EP1578399A4 (en) 2002-12-06 2007-11-28 Isis Pharmaceuticals Inc Methods for rapid identification of pathogens in humans and animals
US8046171B2 (en) 2003-04-18 2011-10-25 Ibis Biosciences, Inc. Methods and apparatus for genetic evaluation
US8057993B2 (en) 2003-04-26 2011-11-15 Ibis Biosciences, Inc. Methods for identification of coronaviruses
US7964343B2 (en) 2003-05-13 2011-06-21 Ibis Biosciences, Inc. Method for rapid purification of nucleic acids for subsequent analysis by mass spectrometry by solution capture
US8158354B2 (en) 2003-05-13 2012-04-17 Ibis Biosciences, Inc. Methods for rapid purification of nucleic acids for subsequent analysis by mass spectrometry by solution capture
US8242254B2 (en) 2003-09-11 2012-08-14 Ibis Biosciences, Inc. Compositions for use in identification of bacteria
US8546082B2 (en) 2003-09-11 2013-10-01 Ibis Biosciences, Inc. Methods for identification of sepsis-causing bacteria
US8097416B2 (en) 2003-09-11 2012-01-17 Ibis Biosciences, Inc. Methods for identification of sepsis-causing bacteria
US8163895B2 (en) 2003-12-05 2012-04-24 Ibis Biosciences, Inc. Compositions for use in identification of orthopoxviruses
US7666592B2 (en) 2004-02-18 2010-02-23 Ibis Biosciences, Inc. Methods for concurrent identification and quantification of an unknown bioagent
US8119336B2 (en) 2004-03-03 2012-02-21 Ibis Biosciences, Inc. Compositions for use in identification of alphaviruses
WO2005117270A2 (en) 2004-05-24 2005-12-08 Isis Pharmaceuticals, Inc. Mass spectrometry with selective ion filtration by digital thresholding
US20050266411A1 (en) 2004-05-25 2005-12-01 Hofstadler Steven A Methods for rapid forensic analysis of mitochondrial DNA
US7811753B2 (en) 2004-07-14 2010-10-12 Ibis Biosciences, Inc. Methods for repairing degraded DNA
CA2600184A1 (en) 2005-03-03 2006-09-08 Isis Pharmaceuticals, Inc. Compositions for use in identification of adventitious viruses
US8084207B2 (en) 2005-03-03 2011-12-27 Ibis Bioscience, Inc. Compositions for use in identification of papillomavirus
AU2006272776B2 (en) 2005-07-21 2012-01-19 Ibis Biosciences, Inc. Methods for rapid identification and quantitation of nucleic acid variants
AU2007353877B2 (en) 2006-09-14 2012-07-19 Ibis Biosciences, Inc. Targeted whole genome amplification method for identification of pathogens
EP2126132B1 (en) 2007-02-23 2013-03-20 Ibis Biosciences, Inc. Methods for rapid foresnsic dna analysis
WO2008151023A2 (en) 2007-06-01 2008-12-11 Ibis Biosciences, Inc. Methods and compositions for multiple displacement amplification of nucleic acids
EP2349549B1 (en) 2008-09-16 2012-07-18 Ibis Biosciences, Inc. Mixing cartridges, mixing stations, and related kits, and system
US8148163B2 (en) 2008-09-16 2012-04-03 Ibis Biosciences, Inc. Sample processing units, systems, and related methods
EP2344893B1 (en) 2008-09-16 2014-10-15 Ibis Biosciences, Inc. Microplate handling systems and methods
JP5413185B2 (en) * 2008-12-25 2014-02-12 Ｊｓｒ株式会社 Negative radiation sensitive composition, cured pattern forming method and cured pattern
EP2396803A4 (en) 2009-02-12 2016-10-26 Ibis Biosciences Inc Ionization probe assemblies
US9393564B2 (en) 2009-03-30 2016-07-19 Ibis Biosciences, Inc. Bioagent detection systems, devices, and methods
WO2011008971A1 (en) 2009-07-17 2011-01-20 Ibis Biosciences, Inc. Lift and mount apparatus
US9194877B2 (en) 2009-07-17 2015-11-24 Ibis Biosciences, Inc. Systems for bioagent indentification
US9416409B2 (en) 2009-07-31 2016-08-16 Ibis Biosciences, Inc. Capture primers and capture sequence linked solid supports for molecular diagnostic tests
EP2488656B1 (en) 2009-10-15 2015-06-03 Ibis Biosciences, Inc. Multiple displacement amplification
ES2626411T3 (en) 2010-03-10 2017-07-25 Ibis Biosciences, Inc. Single-chain circular nucleic acid production
US9068017B2 (en) 2010-04-08 2015-06-30 Ibis Biosciences, Inc. Compositions and methods for inhibiting terminal transferase activity
WO2013036603A1 (en) 2011-09-06 2013-03-14 Ibis Biosciences, Inc. Sample preparation methods
US9970061B2 (en) 2011-12-27 2018-05-15 Ibis Biosciences, Inc. Bioagent detection oligonucleotides
US20150241319A1 (en) 2012-09-26 2015-08-27 Thomas N. Chiesl Swab interface for a microfluidic device
US10649982B2 (en) * 2017-11-09 2020-05-12 Fry Laboratories, LLC Automated database updating and curation

Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6389428B1 (en) * 1998-05-04 2002-05-14 Incyte Pharmaceuticals, Inc. System and method for a precompiled database for biomolecular sequence information
US6553317B1 (en) * 1997-03-05 2003-04-22 Incyte Pharmaceuticals, Inc. Relational database and system for storing information relating to biomolecular sequences and reagents
US20030082539A1 (en) * 2001-06-26 2003-05-01 Ecker David J. Secondary structure defining database and methods for determining identity and geographic origin of an unknown bioagent thereby
US20030187615A1 (en) * 2002-03-26 2003-10-02 John Epler Methods and apparatus for early detection of health-related events in a population
US20050065813A1 (en) * 2003-03-11 2005-03-24 Mishelevich David J. Online medical evaluation system

Patent Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6553317B1 (en) * 1997-03-05 2003-04-22 Incyte Pharmaceuticals, Inc. Relational database and system for storing information relating to biomolecular sequences and reagents
US6389428B1 (en) * 1998-05-04 2002-05-14 Incyte Pharmaceuticals, Inc. System and method for a precompiled database for biomolecular sequence information
US20030082539A1 (en) * 2001-06-26 2003-05-01 Ecker David J. Secondary structure defining database and methods for determining identity and geographic origin of an unknown bioagent thereby
US20030187615A1 (en) * 2002-03-26 2003-10-02 John Epler Methods and apparatus for early detection of health-related events in a population
US20050065813A1 (en) * 2003-03-11 2005-03-24 Mishelevich David J. Online medical evaluation system

Also Published As

Publication number Publication date
WO2005036369A2 (en) 2005-04-21

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