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Published in: Journal of Digital Imaging 4/2013

01-08-2013

A Novel Knowledge Representation Framework for the Statistical Validation of Quantitative Imaging Biomarkers

Authors: Andrew J. Buckler, David Paik, Matt Ouellette, Jovanna Danagoulian, Gary Wernsing, Baris E. Suzek

Published in: Journal of Imaging Informatics in Medicine | Issue 4/2013

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Abstract

Quantitative imaging biomarkers are of particular interest in drug development for their potential to accelerate the drug development pipeline. The lack of consensus methods and carefully characterized performance hampers the widespread availability of these quantitative measures. A framework to support collaborative work on quantitative imaging biomarkers would entail advanced statistical techniques, the development of controlled vocabularies, and a service-oriented architecture for processing large image archives. Until now, this framework has not been developed. With the availability of tools for automatic ontology-based annotation of datasets, coupled with image archives, and a means for batch selection and processing of image and clinical data, imaging will go through a similar increase in capability analogous to what advanced genetic profiling techniques have brought to molecular biology. We report on our current progress on developing an informatics infrastructure to store, query, and retrieve imaging biomarker data across a wide range of resources in a semantically meaningful way that facilitates the collaborative development and validation of potential imaging biomarkers by many stakeholders. Specifically, we describe the semantic components of our system, QI-Bench, that are used to specify and support experimental activities for statistical validation in quantitative imaging
Literature
1.
go back to reference Woodcock J, Woosley R: The FDA critical path initiative and its influence on new drug development. Annu Rev Med 59:1–12, 2008PubMedCrossRef Woodcock J, Woosley R: The FDA critical path initiative and its influence on new drug development. Annu Rev Med 59:1–12, 2008PubMedCrossRef
2.
go back to reference Pien HH, et al: Using imaging biomarkers to accelerate drug development and clinical trials. Drug Discov Today 10(4):259–266, 2005PubMedCrossRef Pien HH, et al: Using imaging biomarkers to accelerate drug development and clinical trials. Drug Discov Today 10(4):259–266, 2005PubMedCrossRef
3.
go back to reference Buckler AJ, et al: A collaborative enterprise for multi-stakeholder participation in the advancement of quantitative imaging. Radiology 258(3):906–914, 2011PubMedCrossRef Buckler AJ, et al: A collaborative enterprise for multi-stakeholder participation in the advancement of quantitative imaging. Radiology 258(3):906–914, 2011PubMedCrossRef
4.
go back to reference Shankar LK, et al: Considerations for the use of imaging tools for phase II treatment trials in oncology. Clin Cancer Res: Off J American Assoc Cancer Res 15(6):1891–1897, 2009CrossRef Shankar LK, et al: Considerations for the use of imaging tools for phase II treatment trials in oncology. Clin Cancer Res: Off J American Assoc Cancer Res 15(6):1891–1897, 2009CrossRef
5.
go back to reference Jaffe CC: Measures of response: RECIST, WHO, and new alternatives. J Clin Oncol 24(20):3245–3251, 2006PubMedCrossRef Jaffe CC: Measures of response: RECIST, WHO, and new alternatives. J Clin Oncol 24(20):3245–3251, 2006PubMedCrossRef
8.
go back to reference Moncada V, Srivastava S: Biomarkers in oncology research and treatment: early detection research network: a collaborative approach. Biomark Med 2(2):181–195, 2008PubMedCrossRef Moncada V, Srivastava S: Biomarkers in oncology research and treatment: early detection research network: a collaborative approach. Biomark Med 2(2):181–195, 2008PubMedCrossRef
9.
go back to reference Yang IS, et al: IDBD: infectious disease biomarker database. Nucleic Acids Res 36(Database issue):D455–D460, 2008PubMed Yang IS, et al: IDBD: infectious disease biomarker database. Nucleic Acids Res 36(Database issue):D455–D460, 2008PubMed
10.
go back to reference Wong D: Liaison Committee Discusses Possible Radiotracer Sharing Clearinghouse, in American College of Neuropsychopharmacology2006 Wong D: Liaison Committee Discusses Possible Radiotracer Sharing Clearinghouse, in American College of Neuropsychopharmacology2006
11.
go back to reference Wong DF: Imaging in drug discovery, preclinical, and early clinical development. J Nucl Med: Off Pub Soc Nucl Med 49(6):26N–28N, 2008 Wong DF: Imaging in drug discovery, preclinical, and early clinical development. J Nucl Med: Off Pub Soc Nucl Med 49(6):26N–28N, 2008
12.
go back to reference Brown MS, et al: Database design and implementation for quantitative image analysis research. IEEE Trans Inf Technol Biomed 9(1):99–108, 2005PubMedCrossRef Brown MS, et al: Database design and implementation for quantitative image analysis research. IEEE Trans Inf Technol Biomed 9(1):99–108, 2005PubMedCrossRef
13.
go back to reference Maier D, et al: Knowledge management for systems biology a general and visually driven framework applied to translational medicine. BMC Syst Biol 5:38, 2011PubMedCrossRef Maier D, et al: Knowledge management for systems biology a general and visually driven framework applied to translational medicine. BMC Syst Biol 5:38, 2011PubMedCrossRef
14.
go back to reference Sheikh HR, Sabir MF, Bovik AC: A statistical evaluation of recent full reference image quality assessment algorithms. IEEE Trans Image Process: Publ IEEE Signal Process Soc 15(11):3440–3451, 2006CrossRef Sheikh HR, Sabir MF, Bovik AC: A statistical evaluation of recent full reference image quality assessment algorithms. IEEE Trans Image Process: Publ IEEE Signal Process Soc 15(11):3440–3451, 2006CrossRef
15.
go back to reference Toyohara J, et al: Evaluation of 4'-[methyl-14C]thiothymidine for in vivo DNA synthesis imaging. J Nuclear Medicine: Off Publ Soc Nucl Med 47(10):1717–1722, 2006 Toyohara J, et al: Evaluation of 4'-[methyl-14C]thiothymidine for in vivo DNA synthesis imaging. J Nuclear Medicine: Off Publ Soc Nucl Med 47(10):1717–1722, 2006
16.
go back to reference Yuk SH, et al: Glycol chitosan/heparin immobilized iron oxide nanoparticles with a tumor-targeting characteristic for magnetic resonance imaging. Biomacromolecules 12(6):2335–2343, 2011PubMedCrossRef Yuk SH, et al: Glycol chitosan/heparin immobilized iron oxide nanoparticles with a tumor-targeting characteristic for magnetic resonance imaging. Biomacromolecules 12(6):2335–2343, 2011PubMedCrossRef
17.
go back to reference Veenendaal LM, et al: In vitro and in vivo studies of a VEGF121/rGelonin chimeric fusion toxin targeting the neovasculature of solid tumors. Proc Natl Acad Sci U S A 99(12):7866–7871, 2002PubMedCrossRef Veenendaal LM, et al: In vitro and in vivo studies of a VEGF121/rGelonin chimeric fusion toxin targeting the neovasculature of solid tumors. Proc Natl Acad Sci U S A 99(12):7866–7871, 2002PubMedCrossRef
18.
go back to reference Wen X, et al: Biodistribution, pharmacokinetics, and nuclear imaging studies of 111In-labeled rGel/BLyS fusion toxin in SCID mice bearing B cell lymphoma. Mol Imaging Biol: MIB: Off Publ Acad Mol Imaging 13(4):721–729, 2011CrossRef Wen X, et al: Biodistribution, pharmacokinetics, and nuclear imaging studies of 111In-labeled rGel/BLyS fusion toxin in SCID mice bearing B cell lymphoma. Mol Imaging Biol: MIB: Off Publ Acad Mol Imaging 13(4):721–729, 2011CrossRef
19.
go back to reference Wang HH, et al: Durable mesenchymal stem cell labelling by using polyhedral superparamagnetic iron oxide nanoparticles. Chemistry 15(45):12417–12425, 2009PubMedCrossRef Wang HH, et al: Durable mesenchymal stem cell labelling by using polyhedral superparamagnetic iron oxide nanoparticles. Chemistry 15(45):12417–12425, 2009PubMedCrossRef
21.
22.
go back to reference Jaffer FA, Weissleder R: Molecular imaging in the clinical arena. JAMA: J American Medical Association 293(7):855–862, 2005CrossRef Jaffer FA, Weissleder R: Molecular imaging in the clinical arena. JAMA: J American Medical Association 293(7):855–862, 2005CrossRef
23.
go back to reference Fleming TR: Surrogate endpoints and FDA's accelerated approval process. Heal Aff 24(1):67–78, 2005CrossRef Fleming TR: Surrogate endpoints and FDA's accelerated approval process. Heal Aff 24(1):67–78, 2005CrossRef
24.
go back to reference Atkinson, A.J.e.a: Biomarkers and surrogate endpoints: preferred definitions and conceptual framework. Clinical pharmacology and therapeutics 69(3):89–95, 2001 Atkinson, A.J.e.a: Biomarkers and surrogate endpoints: preferred definitions and conceptual framework. Clinical pharmacology and therapeutics 69(3):89–95, 2001
25.
26.
go back to reference Lathia CD, et al: The value, qualification, and regulatory use of surrogate end points in drug development. Clin Pharmacol Ther 86(1):32–43, 2009PubMedCrossRef Lathia CD, et al: The value, qualification, and regulatory use of surrogate end points in drug development. Clin Pharmacol Ther 86(1):32–43, 2009PubMedCrossRef
27.
go back to reference Quon A, Gambhir SS: FDG-PET and beyond: molecular breast cancer imaging. J Clin Oncol 23(8):1664–1673, 2005PubMedCrossRef Quon A, Gambhir SS: FDG-PET and beyond: molecular breast cancer imaging. J Clin Oncol 23(8):1664–1673, 2005PubMedCrossRef
28.
go back to reference Smith JJ, Sorensen AG, Thrall JH: Biomarkers in imaging: realizing radiology's future. Radiology 227(3):633–638, 2003PubMedCrossRef Smith JJ, Sorensen AG, Thrall JH: Biomarkers in imaging: realizing radiology's future. Radiology 227(3):633–638, 2003PubMedCrossRef
29.
go back to reference Li W, et al: Noninvasive imaging and quantification of epidermal growth factor receptor kinase activation in vivo. Cancer Res 68(13):4990–4997, 2008PubMedCrossRef Li W, et al: Noninvasive imaging and quantification of epidermal growth factor receptor kinase activation in vivo. Cancer Res 68(13):4990–4997, 2008PubMedCrossRef
30.
go back to reference Klibanov AL: Ligand-carrying gas-filled microbubbles: ultrasound contrast agents for targeted molecular imaging. Bioconjugate Chemistry 16(1):9–17, 2005PubMedCrossRef Klibanov AL: Ligand-carrying gas-filled microbubbles: ultrasound contrast agents for targeted molecular imaging. Bioconjugate Chemistry 16(1):9–17, 2005PubMedCrossRef
31.
go back to reference Hehenberger M: Information Based Medicine: From Biobanks to Biomarkers, 2007, IBM Healthcare & Life Sciences: High Tech Connections (HTC) Forum Hehenberger M: Information Based Medicine: From Biobanks to Biomarkers, 2007, IBM Healthcare & Life Sciences: High Tech Connections (HTC) Forum
32.
go back to reference Sadot A, et al: Toward verified biological models. IEEE/ACM Trans Comput Biol Bioinform 5(2):223–234, 2008PubMedCrossRef Sadot A, et al: Toward verified biological models. IEEE/ACM Trans Comput Biol Bioinform 5(2):223–234, 2008PubMedCrossRef
33.
go back to reference Cavusoglu E.Z.E.a.M.C: A Software Framework for Multiscale and Multilevel Physiological Model Integration and Simulation, in 30th Annual International IEEE EMBS Conference 2008: Vancouver, British Columbia, Canada Cavusoglu E.Z.E.a.M.C: A Software Framework for Multiscale and Multilevel Physiological Model Integration and Simulation, in 30th Annual International IEEE EMBS Conference 2008: Vancouver, British Columbia, Canada
34.
go back to reference Feng D: Molecular Imaging and Biomedical Process Modeling, in 2nd Asia-Pacific Bioinformatics Conference (APBC2004)2004 Feng D: Molecular Imaging and Biomedical Process Modeling, in 2nd Asia-Pacific Bioinformatics Conference (APBC2004)2004
35.
go back to reference Chen J, et al: How Will Bioinformatics Impact Signal Processing Research? IEEE Signal Processing Magazine p. 16–26, 2003 Chen J, et al: How Will Bioinformatics Impact Signal Processing Research? IEEE Signal Processing Magazine p. 16–26, 2003
36.
go back to reference Toretsky J, et al: Preparation of F-18 labeled annexin V: a potential PET radiopharmaceutical for imaging cell death. Nucl Med Biol 31(6):747–752, 2004PubMedCrossRef Toretsky J, et al: Preparation of F-18 labeled annexin V: a potential PET radiopharmaceutical for imaging cell death. Nucl Med Biol 31(6):747–752, 2004PubMedCrossRef
37.
go back to reference Zijlstra, S., J. Gunawan, and W. Burchert, Synthesis and evaluation of a 18F-labelled recombinant annexin-V derivative, for identification and quantification of apoptotic cells with PET. Applied radiation and isotopes : including data, instrumentation and methods for use in agriculture, industry and medicine 58(2): p. 201–7, 2003 Zijlstra, S., J. Gunawan, and W. Burchert, Synthesis and evaluation of a 18F-labelled recombinant annexin-V derivative, for identification and quantification of apoptotic cells with PET. Applied radiation and isotopes : including data, instrumentation and methods for use in agriculture, industry and medicine 58(2): p. 201–7, 2003
38.
go back to reference Zhao B, et al: Evaluating variability in tumor measurements from same-day repeat CT scans of patients with non-small cell lung cancer. Radiology 252(1):263–272, 2009PubMedCrossRef Zhao B, et al: Evaluating variability in tumor measurements from same-day repeat CT scans of patients with non-small cell lung cancer. Radiology 252(1):263–272, 2009PubMedCrossRef
39.
go back to reference Buckler AJ, Boellaard R: Standardization of quantitative imaging: the time is right, and 18F-FDG PET/CT is a good place to start. J Medicine: Off Publ Soc Nucl Med 52(2):171–172, 2011CrossRef Buckler AJ, Boellaard R: Standardization of quantitative imaging: the time is right, and 18F-FDG PET/CT is a good place to start. J Medicine: Off Publ Soc Nucl Med 52(2):171–172, 2011CrossRef
40.
go back to reference Creating the gene ontology resource: design and implementation. Genome Res 11(8): p. 1425–33, 2001 Creating the gene ontology resource: design and implementation. Genome Res 11(8): p. 1425–33, 2001
41.
go back to reference Ashburner M, et al: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25(1):25–29, 2000PubMedCrossRef Ashburner M, et al: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25(1):25–29, 2000PubMedCrossRef
42.
go back to reference Romero-Zaliz RC, et al: A multiobjective evolutionary conceptual clustering methodology for gene annotation within structural databases: a case of study on the gene ontology database. IEEE Trans Evol Comput 12(6):679–701, 2008CrossRef Romero-Zaliz RC, et al: A multiobjective evolutionary conceptual clustering methodology for gene annotation within structural databases: a case of study on the gene ontology database. IEEE Trans Evol Comput 12(6):679–701, 2008CrossRef
43.
go back to reference Brazma A, et al: Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 29(4):365–371, 2001PubMedCrossRef Brazma A, et al: Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 29(4):365–371, 2001PubMedCrossRef
44.
go back to reference Sirota M, et al: Discovery and preclinical validation of drug indications using compendia of public gene expression data. Sci Trans Med 3(96):96ra77, 2011CrossRef Sirota M, et al: Discovery and preclinical validation of drug indications using compendia of public gene expression data. Sci Trans Med 3(96):96ra77, 2011CrossRef
45.
go back to reference Buckler AJ, et al: Quantitative imaging test approval and biomarker qualification: interrelated but distinct activities. Radiology 259(3):875–884, 2011PubMedCrossRef Buckler AJ, et al: Quantitative imaging test approval and biomarker qualification: interrelated but distinct activities. Radiology 259(3):875–884, 2011PubMedCrossRef
46.
go back to reference Buckler AJ, et al: Volumetric CT in lung cancer: an example for the qualification of imaging as a biomarker. Acad Radiol 17(1):107–115, 2010PubMedCrossRef Buckler AJ, et al: Volumetric CT in lung cancer: an example for the qualification of imaging as a biomarker. Acad Radiol 17(1):107–115, 2010PubMedCrossRef
47.
go back to reference Buckler AJ, et al: The use of volumetric CT as an imaging biomarker in lung cancer. Acad Radiol 17(1):100–106, 2010PubMedCrossRef Buckler AJ, et al: The use of volumetric CT as an imaging biomarker in lung cancer. Acad Radiol 17(1):100–106, 2010PubMedCrossRef
48.
go back to reference Buckler AJ, et al: Datasets for the qualification of volumetric CT as a quantitative imaging biomarker in lung cancer. Opt Express 18(14):15267–15282, 2010PubMedCrossRef Buckler AJ, et al: Datasets for the qualification of volumetric CT as a quantitative imaging biomarker in lung cancer. Opt Express 18(14):15267–15282, 2010PubMedCrossRef
49.
go back to reference Buckler AJ, Schwartz LH, Petrick N, McNitt-Gray M, Zhao B, Fenimore C, Reeves AP, Mozley PD, Avila RS: Datasets for the qualification of CT as a quantitative imaging biomarker in lung cancer. Opt Express 18(14):16, 2010CrossRef Buckler AJ, Schwartz LH, Petrick N, McNitt-Gray M, Zhao B, Fenimore C, Reeves AP, Mozley PD, Avila RS: Datasets for the qualification of CT as a quantitative imaging biomarker in lung cancer. Opt Express 18(14):16, 2010CrossRef
50.
go back to reference Mozley PD, et al: Change in lung tumor volume as a biomarker of treatment response: a critical review of the evidence. Ann Oncol 21(9):1751–1755, 2010PubMedCrossRef Mozley PD, et al: Change in lung tumor volume as a biomarker of treatment response: a critical review of the evidence. Ann Oncol 21(9):1751–1755, 2010PubMedCrossRef
51.
go back to reference Liu T, et al: The Imaging Biomarker Ontology: Ontology-based Support for Imaging Biomarker Research, in Society for Imaging Informatics in Medicine 2011 Annual Meeting2011 Liu T, et al: The Imaging Biomarker Ontology: Ontology-based Support for Imaging Biomarker Research, in Society for Imaging Informatics in Medicine 2011 Annual Meeting2011
52.
go back to reference Noy NF and DL McGuinness: A Guide to Creating Your First Ontology. Stanford Knowledge Systems Laboratory technical report KSL-01-05 and Stanford Medical Informatics technical report SMI-2001-0880, 2001 Noy NF and DL McGuinness: A Guide to Creating Your First Ontology. Stanford Knowledge Systems Laboratory technical report KSL-01-05 and Stanford Medical Informatics technical report SMI-2001-0880, 2001
53.
go back to reference Rubin DL: Creating and curating a terminology for radiology: ontology modeling and analysis. J Digital Imaging Off J Soc Comput Appl Radiol 21(4):355–362, 2008CrossRef Rubin DL: Creating and curating a terminology for radiology: ontology modeling and analysis. J Digital Imaging Off J Soc Comput Appl Radiol 21(4):355–362, 2008CrossRef
54.
go back to reference Rubin DL, Noy NF, Musen MA: Protege: a tool for managing and using terminology in radiology applications. J Digital Imaging Off J Soc Comput Appl Radiol 20(Suppl 1):34–46, 2007CrossRef Rubin DL, Noy NF, Musen MA: Protege: a tool for managing and using terminology in radiology applications. J Digital Imaging Off J Soc Comput Appl Radiol 20(Suppl 1):34–46, 2007CrossRef
55.
go back to reference Musen MA: Domain ontologies in software engineering: use of Protege with the EON architecture. Methods Inform Med 37(4–5):540–550, 1998 Musen MA: Domain ontologies in software engineering: use of Protege with the EON architecture. Methods Inform Med 37(4–5):540–550, 1998
56.
go back to reference Musen MA, et al: PROTEGE-II: computer support for development of intelligent systems from libraries of components. Medinfo. MEDINFO 8 Pt 1: p. 766–70, 1995 Musen MA, et al: PROTEGE-II: computer support for development of intelligent systems from libraries of components. Medinfo. MEDINFO 8 Pt 1: p. 766–70, 1995
61.
go back to reference Sansone SA, et al: The first RSBI (ISA-TAB) workshop: “can a simple format work for complex studies?”. OMICS 12(2):143–149, 2008PubMedCrossRef Sansone SA, et al: The first RSBI (ISA-TAB) workshop: “can a simple format work for complex studies?”. OMICS 12(2):143–149, 2008PubMedCrossRef
63.
go back to reference Sargent DJ, et al: Validation of novel imaging methodologies for use as cancer clinical trial end-points. Eur J Cancer 45(2):290–299, 2009PubMedCrossRef Sargent DJ, et al: Validation of novel imaging methodologies for use as cancer clinical trial end-points. Eur J Cancer 45(2):290–299, 2009PubMedCrossRef
68.
go back to reference Tirmizi SH, et al: Mapping between the OBO and OWL ontology languages. J Biomed Semantics 2(Suppl 1):S3, 2011PubMedCrossRef Tirmizi SH, et al: Mapping between the OBO and OWL ontology languages. J Biomed Semantics 2(Suppl 1):S3, 2011PubMedCrossRef
79.
go back to reference Chapman AB, Wei W: Imaging approaches to patients with polycystic kidney disease. Semin Nephrol 31(3):237–244, 2011PubMedCrossRef Chapman AB, Wei W: Imaging approaches to patients with polycystic kidney disease. Semin Nephrol 31(3):237–244, 2011PubMedCrossRef
85.
go back to reference Vandervalk BP, McCarthy EL, Wilkinson MD: SHARE: a semantic web query engine for bioinformatics (Defense). Integr VLSI J 5926:367–369, 2009 Vandervalk BP, McCarthy EL, Wilkinson MD: SHARE: a semantic web query engine for bioinformatics (Defense). Integr VLSI J 5926:367–369, 2009
86.
go back to reference Chepelev L, et al: Prototype semantic infrastructure for automated small molecule classification and annotation in lipidomics. BMC Bioinforma 12(1):303, 2011CrossRef Chepelev L, et al: Prototype semantic infrastructure for automated small molecule classification and annotation in lipidomics. BMC Bioinforma 12(1):303, 2011CrossRef
87.
go back to reference Laurila JB, et al: Algorithms and semantic infrastructure for mutation impact extraction and grounding. BMC Genomics 11(Suppl 4):S24, 2010PubMedCrossRef Laurila JB, et al: Algorithms and semantic infrastructure for mutation impact extraction and grounding. BMC Genomics 11(Suppl 4):S24, 2010PubMedCrossRef
Metadata
Title
A Novel Knowledge Representation Framework for the Statistical Validation of Quantitative Imaging Biomarkers
Authors
Andrew J. Buckler
David Paik
Matt Ouellette
Jovanna Danagoulian
Gary Wernsing
Baris E. Suzek
Publication date
01-08-2013
Publisher
Springer US
Published in
Journal of Imaging Informatics in Medicine / Issue 4/2013
Print ISSN: 2948-2925
Electronic ISSN: 2948-2933
DOI
https://doi.org/10.1007/s10278-013-9598-3

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