An ICT infrastructure to integrate clinical and molecular data in oncology research

BMC Bioinformatics

Volumn 13, Issue SUPPL.4, 2012, Pages

  Segagni, Daniele ^a   Tibollo, Valentina ^a   Dagliati, Arianna ^b   Zambelli, Alberto ^a   Priori, Silvia G ^a   Bellazzi, Riccardo ^c  

^a IRCCS   (Italy)

^b SCUOLA UNIVERSITARIA SUPERIORE IUSS PAVIA   (Italy)

^c UNIVERSITY OF PAVIA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ANONYMIZATION; BIOINFORMATICS DATA; BIOINFORMATICS TOOLS; BIOLOGICAL SAMPLES; BREAST CANCER DIAGNOSIS; CLINICAL INFORMATION; CLINICAL TESTS; HOSPITAL INFORMATION; ICT INFRASTRUCTURES; INFORMATICS; INTEGRATED INFORMATIONS; INTEGRATED RESEARCH; INTEGRATION PROCESS; MALIGNANT TUMORS; MEDICAL RECORD; MOLECULAR DATA; MULTIPLE SOURCE; NATURAL LANGUAGE PROCESSING; OPEN SOURCES; PLUG-INS; QUERY TOOLS; RESEARCH CENTER; RESEARCH DATA; TEMPORAL QUERIES; TRANSLATIONAL RESEARCH;

BIOINFORMATICS; DATA WAREHOUSES; DIAGNOSIS; DISEASES; HOSPITALS; INFORMATION TECHNOLOGY; MEDICAL COMPUTING; NATURAL LANGUAGE PROCESSING SYSTEMS; ONCOLOGY; QUERY PROCESSING; RECORDS MANAGEMENT; RESEARCH;

DATA INTEGRATION;

ARTICLE; BREAST TUMOR; COMPUTER PROGRAM; FACTUAL DATABASE; HOSPITAL INFORMATION SYSTEM; HUMAN; INFORMATION RETRIEVAL; NATURAL LANGUAGE PROCESSING; ONCOLOGY; PATHOLOGY; STATISTICS; TRANSLATIONAL RESEARCH;

BREAST NEOPLASMS; DATABASES, FACTUAL; HOSPITAL INFORMATION SYSTEMS; HUMANS; INFORMATION STORAGE AND RETRIEVAL; MEDICAL ONCOLOGY; NATURAL LANGUAGE PROCESSING; SOFTWARE; TRANSLATIONAL MEDICAL RESEARCH;

EID: 84864925958     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-13-S4-S5     Document Type: Article

References (25)

1. Murphy SN, Mendis M, Hackett K, Kuttan R, Pan W, Phillips LC, Gainer V, Berkowicz D, Glaser JP, Kohane I, Chueh HC. Architecture of the open-source clinical research chart from Informatics for Integrating Biology and the Bedside. AMIA Annu Symp Proc 2007, 548-552. PMC2655844, 18693896.
2. i2b2 web site. (last accessed November 23rd 2011)., https://www.i2b2.org
3. National Center of Biomedical Computing web site. (last accessed Noverber 23rd 2011)., http://www.ncbcs.org
4. Murphy SN, Weber G, Mendis M, Gainer V, Chueh HC, Churchill S, Kohane I. Serving the enterprise and beyond with informatics for integrating biology and the bedside (i2b2). J Am Med Inform Assoc 2010, 17(2):124-130. 10.1136/jamia.2009.000893, 3000779, 20190053.
5. Kimball R, Ross M. The Data Warehouse ETL Toolkit 2008, Wiley, 2.
6. Mate S, Bürkle T, Köpcke F, Breil B, Wullich B, Dugas M, Prokosch HU, Ganslandt T. Populating the i2b2 database with heterogeneous EMR data: a semantic network approach. Stud Health Technol Inform 2011, 169:502-506.
7. Adamusiak T, Burdett T, Kurbatova N, Joeri van der Velde K, Abeygunawardena N, Antonakaki D, Kapushesky M, Parkinson H, Swertz MA. OntoCAT--simple ontology search and integration in Java, R and REST/JavaScript. BMC Bioinformatics 2011, 12:218. 10.1186/1471-2105-12-218, 3129328, 21619703.
8. Murphy SN, Gainer V, Mendis M, Churchill S, Kohane I. Strategies for maintaining patient privacy in i2b2. J Am Med Inform Assoc 2011,
9. Malin B, Loukides G, Benitez K, Clayton EW. Identifiability in biobanks: models, measures, and mitigation strategies. Hum Genet 2011, 130(3):383-392. 10.1007/s00439-011-1042-5, 21739176.
10. Pentaho Data Integration Kettle Documentation. (last accessed November 23rd 2011)., http://kettle.pentaho.com
11. Bouman R, van Dongen J. Pentaho Solutions 2009, Wiley.
12. Google Web Toolkit web site. (last accessed November 23rd 2011)., http://code.google.com/webtoolkit/
13. Childs LC, Enelow R, Simonsen L, Heintzelman NH, Kowalski KM, Taylor RJ. Description of a rule-based system for the i2b2 challenge in natural language processing for clinical data. J Am Med Inform Assoc 2009, 16(4):571-575. 10.1197/jamia.M3083, 2705261, 19390103.
14. Rosenbloom ST, Brown SH, Froehling D, Bauer BA, Wahner-Roedler DL, Gregg WM, Elkin PL. Using SNOMED CT to represent two interface terminologies. J Am Med Inform Assoc 2009, 16(1):81-88. 10.1197/jamia.M2694, 2605600, 18952944.
15. Sobin LH, Gospodarowicz MK, Wittekind C. TNM Classification of Malignant Tumours 2009, Wiley, 7.
16. Going JJ. Observer prediction of HER2 amplification in HercepTest 2+ breast cancers as a potential audit instrument. Histopathology 2011, 59(2):333-335.
17. de Azambuja E, Cardoso F, de Castro G, Colozza M, Mano MS, Durbecq V, Sotiriou C, Larsimont D, Piccart-Gebhart MJ, Paesmans M. Ki-67 as prognostic marker in early breast cancer: a meta-analysis of published studies involving 12,155 patients. Br J Cancer 2007, 96(10):1504-1513. 10.1038/sj.bjc.6603756, 2359936, 17453008.
18. Cunningham H, Maynard D, Bontcheva K. Text Processing with GATE (Version 6) 2011, University of Sheffield Department of Computer Science.
19. Noy NF, Shah NH, Whetzel PL, Dai B, Dorf M, Griffith N, Jonquet C, Rubin DL, Storey MA, Chute CG, Musen MA. BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Res 2009, 37(Web Server issue):W170-W173. 2703982, 19483092.
20. Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T, Musen MA. BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res 2011, 39(Web Server issue):W541-W545. 3125807, 21672956.
21. Bioportal Ontology OWL file. (last accessed December 12th 2011)., http://bioportal.bioontology.org/ontologies/2086?p=terms
22. Segagni D, Ferrazzi F, Larizza C, Tibollo V, Napolitano C, Priori SG, Bellazzi R. R engine cell: integrating R into the i2b2 software infrastructure. J Am Med Inform Assoc 2011, 18(3):314-317. 10.1136/jamia.2010.007914, 3078677, 21262924.
23. I2b2 community website. (last accessed November 23rd 2011)., https://community.i2b2.org
24. Weber GM, Murphy SN, McMurry AJ, Macfadden D, Nigrin DJ, Churchill S, Kohane IS. The Shared Health Research Information Network (SHRINE): a prototype federated query tool for clinical data repositories. J Am Med Inform Assoc 2009, 16(5):624-630. 10.1197/jamia.M3191, 2744712, 19567788.
25. Phillips LC, Minovitsky S, Ratnere I, Dubchak I, Kohane I, Murphy SN. Use Genomic Variants in Informatics for Integrating Biology and the Bedside (i2b2). AMIA Proceedings Library: 48-52 T2011