publication . Article . Other literature type . 2018

Labeling for Big Data in radiation oncology: The Radiation Oncology Structures ontology.

Bastien Rance; Jean-Emmanuel Bibault;
Open Access
  • Published: 19 Jan 2018
  • Publisher: Public Library of Science (PLoS)
Abstract
Purpose Leveraging Electronic Health Records (EHR) and Oncology Information Systems (OIS) has great potential to generate hypotheses for cancer treatment, since they directly provide medical data on a large scale. In order to gather a significant amount of patients with a high level of clinical details, multicenter studies are necessary. A challenge in creating high quality Big Data studies involving several treatment centers is the lack of semantic interoperability between data sources. We present the ontology we developed to address this issue. Methods Radiation Oncology anatomical and target volumes were categorized in anatomical and treatment planning classe...
Subjects
free text keywords: General Biochemistry, Genetics and Molecular Biology, General Agricultural and Biological Sciences, General Medicine, Research Article, Medicine and Health Sciences, Oncology, Cancer Treatment, Radiation Therapy, Clinical Medicine, Clinical Oncology, Biology and Life Sciences, Anatomy, Lymphatic System, Lymph Nodes, Computer and Information Sciences, Data Management, Ontologies, Head, Neck, Information Technology, Data Mining, Medicine, R, Science, Q
34 references, page 1 of 3

1 Chen C, He M, Zhu Y, Shi L, Wang X. Five critical elements to ensure the precision medicine. Cancer Metastasis Rev. 2015;34: 313–318. doi: 10.1007/s10555-015-9555-3 25920354 [PubMed]

2 Wilkinson MD, Dumontier M, Aalbersberg IJJ, Appleton G, Axton M, Baak A, et al The FAIR Guiding Principles for scientific data management and stewardship. Sci Data. 2016;3: 160018 doi: 10.1038/sdata.2016.18 26978244 [OpenAIRE] [PubMed]

3 Santanam L, Hurkmans C, Mutic S, van Vliet-Vroegindeweij C, Brame S, Straube W, et al Standardizing Naming Conventions in Radiation Oncology. Int J Radiat Oncol Biol Phys. 2012;83: 1344–1349. doi: 10.1016/j.ijrobp.2011.09.054 22245204 [OpenAIRE] [PubMed]

4 AAPM Committee Tree [Internet]. [cited 22 Jul 2017]. http://www.aapm.org/org/structure/?committee_code=TG263

5 Noy NF, Musen MA, Mejino JLV, Rosse C. Pushing the envelope: challenges in a frame-based representation of human anatomy [Internet]. [cited 25 Apr 2017]. Available: http://www.sciencedirect.com/science/article/pii/S0169023X03001253

6 Rubin DL. Creating and curating a terminology for radiology: ontology modeling and analysis. J Digit Imaging. 2008;21: 355–362. doi: 10.1007/s10278-007-9073-0 17874267 [OpenAIRE] [PubMed]

7 Hwang KH, Lee H, Koh G, Willrett D, Rubin DL. Building and Querying RDF/OWL Data base of Semantically Annotated Nuclear Medicine Images. J Digit Imaging. 2017;30: 4–10. doi: 10.1007/s10278-016-9916-7 27785632 [OpenAIRE] [PubMed]

8 Fact SheetUMLS® Metathesaurus® [Internet]. [cited 7 Mar 2016]. https://www.nlm.nih.gov/pubs/factsheets/umlsmeta.html

9 Radiation Oncology Ontology—Summary | NCBO BioPortal [Internet]. [cited 7 Mar 2016]. http://bioportal.bioontology.org/ontologies/ROO

10 Grégoire V, Ang K, Budach W, Grau C, Hamoir M, Langendijk JA, et al Delineation of the neck node levels for head and neck tumors: a 2013 update. DAHANCA, EORTC, HKNPCSG, NCIC CTG, NCRI, RTOG, TROG consensus guidelines. Radiother Oncol J Eur Soc Ther Radiol Oncol. 2014;110: 172–181. doi: 10.1016/j.radonc.2013.10.010 24183870 [PubMed]

11 Rusch VW, Asamura H, Watanabe H, Giroux DJ, Rami-Porta R, Goldstraw P, et al The IASLC lung cancer staging project: a proposal for a new international lymph node map in the forthcoming seventh edition of the TNM classification for lung cancer. J Thorac Oncol Off Publ Int Assoc Study Lung Cancer. 2009;4: 568–577. doi: 10.1097/JTO.0b013e3181a0d82e 19357537 [OpenAIRE] [PubMed]

12 Zapletal E, Rodon N, Grabar N, Degoulet P. Methodology of integration of a clinical data warehouse with a clinical information system: the HEGP case. Stud Health Technol Inform. 2010;160: 193–197. 20841676 [OpenAIRE] [PubMed]

13 Rance B, Canuel V, Countouris H, Laurent-Puig P, Burgun A. Integrating Heterogeneous Biomedical Data for Cancer Research: the CARPEM infrastructure. Appl Clin Inform. 2016;7: 260–274. doi: 10.4338/ACI-2015-09-RA-0125 27437039 [OpenAIRE] [PubMed]

14 Jannot A, Zapletal E, Avillach P, Mamzer M, Burgun A, Degoulet P. The Georges Pompidou University Hospital Clinical Data Warehouse: A 8-years follow-up experience. Int J Med Inform, In Press.

15 Varian Incorporated. Varian Developers Forum. In: CodePlex [Internet]. [cited 15 Ap r 2017]. https://variandeveloper.codeplex.com/Wikipage?ProjectName=variandeveloper

34 references, page 1 of 3
Abstract
Purpose Leveraging Electronic Health Records (EHR) and Oncology Information Systems (OIS) has great potential to generate hypotheses for cancer treatment, since they directly provide medical data on a large scale. In order to gather a significant amount of patients with a high level of clinical details, multicenter studies are necessary. A challenge in creating high quality Big Data studies involving several treatment centers is the lack of semantic interoperability between data sources. We present the ontology we developed to address this issue. Methods Radiation Oncology anatomical and target volumes were categorized in anatomical and treatment planning classe...
Subjects
free text keywords: General Biochemistry, Genetics and Molecular Biology, General Agricultural and Biological Sciences, General Medicine, Research Article, Medicine and Health Sciences, Oncology, Cancer Treatment, Radiation Therapy, Clinical Medicine, Clinical Oncology, Biology and Life Sciences, Anatomy, Lymphatic System, Lymph Nodes, Computer and Information Sciences, Data Management, Ontologies, Head, Neck, Information Technology, Data Mining, Medicine, R, Science, Q
34 references, page 1 of 3

1 Chen C, He M, Zhu Y, Shi L, Wang X. Five critical elements to ensure the precision medicine. Cancer Metastasis Rev. 2015;34: 313–318. doi: 10.1007/s10555-015-9555-3 25920354 [PubMed]

2 Wilkinson MD, Dumontier M, Aalbersberg IJJ, Appleton G, Axton M, Baak A, et al The FAIR Guiding Principles for scientific data management and stewardship. Sci Data. 2016;3: 160018 doi: 10.1038/sdata.2016.18 26978244 [OpenAIRE] [PubMed]

3 Santanam L, Hurkmans C, Mutic S, van Vliet-Vroegindeweij C, Brame S, Straube W, et al Standardizing Naming Conventions in Radiation Oncology. Int J Radiat Oncol Biol Phys. 2012;83: 1344–1349. doi: 10.1016/j.ijrobp.2011.09.054 22245204 [OpenAIRE] [PubMed]

4 AAPM Committee Tree [Internet]. [cited 22 Jul 2017]. http://www.aapm.org/org/structure/?committee_code=TG263

5 Noy NF, Musen MA, Mejino JLV, Rosse C. Pushing the envelope: challenges in a frame-based representation of human anatomy [Internet]. [cited 25 Apr 2017]. Available: http://www.sciencedirect.com/science/article/pii/S0169023X03001253

6 Rubin DL. Creating and curating a terminology for radiology: ontology modeling and analysis. J Digit Imaging. 2008;21: 355–362. doi: 10.1007/s10278-007-9073-0 17874267 [OpenAIRE] [PubMed]

7 Hwang KH, Lee H, Koh G, Willrett D, Rubin DL. Building and Querying RDF/OWL Data base of Semantically Annotated Nuclear Medicine Images. J Digit Imaging. 2017;30: 4–10. doi: 10.1007/s10278-016-9916-7 27785632 [OpenAIRE] [PubMed]

8 Fact SheetUMLS® Metathesaurus® [Internet]. [cited 7 Mar 2016]. https://www.nlm.nih.gov/pubs/factsheets/umlsmeta.html

9 Radiation Oncology Ontology—Summary | NCBO BioPortal [Internet]. [cited 7 Mar 2016]. http://bioportal.bioontology.org/ontologies/ROO

10 Grégoire V, Ang K, Budach W, Grau C, Hamoir M, Langendijk JA, et al Delineation of the neck node levels for head and neck tumors: a 2013 update. DAHANCA, EORTC, HKNPCSG, NCIC CTG, NCRI, RTOG, TROG consensus guidelines. Radiother Oncol J Eur Soc Ther Radiol Oncol. 2014;110: 172–181. doi: 10.1016/j.radonc.2013.10.010 24183870 [PubMed]

11 Rusch VW, Asamura H, Watanabe H, Giroux DJ, Rami-Porta R, Goldstraw P, et al The IASLC lung cancer staging project: a proposal for a new international lymph node map in the forthcoming seventh edition of the TNM classification for lung cancer. J Thorac Oncol Off Publ Int Assoc Study Lung Cancer. 2009;4: 568–577. doi: 10.1097/JTO.0b013e3181a0d82e 19357537 [OpenAIRE] [PubMed]

12 Zapletal E, Rodon N, Grabar N, Degoulet P. Methodology of integration of a clinical data warehouse with a clinical information system: the HEGP case. Stud Health Technol Inform. 2010;160: 193–197. 20841676 [OpenAIRE] [PubMed]

13 Rance B, Canuel V, Countouris H, Laurent-Puig P, Burgun A. Integrating Heterogeneous Biomedical Data for Cancer Research: the CARPEM infrastructure. Appl Clin Inform. 2016;7: 260–274. doi: 10.4338/ACI-2015-09-RA-0125 27437039 [OpenAIRE] [PubMed]

14 Jannot A, Zapletal E, Avillach P, Mamzer M, Burgun A, Degoulet P. The Georges Pompidou University Hospital Clinical Data Warehouse: A 8-years follow-up experience. Int J Med Inform, In Press.

15 Varian Incorporated. Varian Developers Forum. In: CodePlex [Internet]. [cited 15 Ap r 2017]. https://variandeveloper.codeplex.com/Wikipage?ProjectName=variandeveloper

34 references, page 1 of 3
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