CytometryML, an XML Format Based on DICOM and FCS for Analytical cytology Data

Cytometry Part A

Volumn 54, Issue 1, 2003, Pages 56-65

  Leif, Robert C ^a   Leif, Suzanne B ^a   Leif, Stephanie H ^a  

^a Newport Instruments   (United States)

Author keywords

Cytometry Markup Language (Cytometry ML); Digital Imaging and Communications in Medicine (DICOM); Extensible Markup Language (XML); Flow Cytometry Standard (FCS); Schema; Standards; Waveform

Indexed keywords

ARTICLE; CELL SUBPOPULATION; COMPUTER ANALYSIS; COMPUTER LANGUAGE; COMPUTER PROGRAM; CYTOMETRY; CYTOMETRY MARKUP LANGUAGE; DIGITAL IMAGING AND COMMUNICATIONS IN MEDICINE; FLOW CYTOMETRY; FLOW CYTOMETRY STANDARD; IMAGE ANALYSIS; INFORMATION PROCESSING; LASER SCANNING CYTOMETRY; MARKUP LANGUAGE; MATHEMATICAL MARKUP LANGUAGE; MICROSCOPIC IMAGE CYTOMETRY; PRIORITY JOURNAL; STANDARD; WAVEFORM;

EID: 0346874502     PISSN: 15524922     EISSN: None     Source Type: Journal    
DOI: 10.1002/cyto.a.10043     Document Type: Article

References (48)

1. Imamura T, Dillaway B, Simon E. XML encryption syntax and processing. In: Eastlake D, Reagle J., editors. W3C recommendation, 10 December 2002. Available from http://www.w3.org/TR/2002/REC-xmlenc-core-2002/210
2. Boyer J, Hughes M, Reagle J. XML-Signature XPath filter 2.0. W3C Recommendation 08 November 2002. Available from: http://www.w3.org/TR/2002/REC-xmldsig-filter2-20021108/
3. Dean PN, Bagwell CB, Lindmo T, Murphy RF, Salzman GC (Data File Standards Committee). Data file standard for flow cytometry. Cytom 1990;11:323-332.
4. Leif RC, Rios R, Becker MC, Becker CK, Self JT, Leif SB. The creation of a laboratory instrument quality monitoring system with AdaSAGE. In: Askura T, Farkas DL, Leif RC, Priezzhev AV, Tromberg BJ, Katzir A, editors. Advanced techniques in analytical cytology, optical diagnosis of living cells and biofluids. Progress in biomedical optics. Volume 2678. Bellingham, WA: SPIE Proceedings; 1996. p 232-239.
5. Seamer LC, Bagwell CB, Barden L, Redelman D, Salzman GC, Wood JC, Murphy RF. Proposed new data file standard for flow cytometry, version FCS 3.0. Cytometry 1997;28:118-122.
6. General principles of software validation; final guidance for industry and FDA staff. Document issued 11 January 2002. Washington, DC: US Department of Health and Human Services, Food and Drug Administration, Center for Devices and Radiological Health, Center for Biologics Evaluation and Research; 2002. Available from: http://www.fda.gov/cdrh/comp/guidance/938.pdf
7. Guidance for TDA reviewers and industry guidance for the content of premarket submissions for software contained in medical devices. Document issued 29 May 1998. Washington, DC: US Department of Health and Human Services, Food and Drug Administration, Center for Devices and Radiological Health, Office of Device Evaluation; 1998. Available from: http://www.fda.gov/cdrh/ode/57.html
8. Leif RC, Leif SB. The evolution of flow cytometry standard, FCS3.0, into a DICOM-compatible format. In: Priezzhev AV, Asakura T, Leif RC, editors. Optical diagnostics of biological fluids and advanced techniques in analytical cytology. Volume 2982. Bellingham, WA: SPIE Proceedings; 1997. p 354-366.
9. Leif RC, Leif SB. A DICOM compatible format for analytical cytology data. In: Farkas DL, Leif RC, Tromberg BJ, editors. Optical investigations of cells in vitro and in vivo. Volume 3260. Bellingham, WA: SPIE Proceedings; 1998. p 282-289.
10. Leif RC, Leif SB. A DICOM compatible format for analytical cytology data, that can be expressed in XML. In: Farkas DL, Leif RC, editors. Optical diagnostics of living cells IV. Volume 4260. Bellingham, WA: SPIE Proceedings; 2001. p 238-248.
11. Murphy RF. International Society for Analytical Cytology, data standards committee meeting minutes, 4-5 January 2002. Available from: http://www.isac-net.org/
12. Online Edition of the Unicode Standard. Version 3.0. Available from: http://www.unicode.org/unicode/uni2book/ch03.pdf. p 37.
13. Programming with the general-purpose instructions. In: IA-32 Intel architecture software developer's manual. Volume 1. Basic architecture; 2002. Available from: www.intel.com/design/pentium4/manuals/24547011.pdf.
14. MPC823 support team. Endian modes. In: PowerPC MPC823 reference manual. Accessed November 2002. Available from: http://e-www.motorola.com/brdata/PDFDB/docs/MPC823UM.pdf
15. Kamentsky LA. Methods and apparatus for measuring multiple optical properties of biological specimens. US patent 5,072,382; 1991.
16. Kamentsky LA, Kamentsky LD, Fletcher JA, Kurose A, Sasaki K. Methods for automatic multiparameter analysis of fluorescence in situ hybridized specimens with a laser scanning cytometer. Cytometry 1997;27:117-125.
17. Buetow K. Combining bioinformatics and genomics to gain insight into the etiology of cancer. ISAC XXI Lectures Online. Special session on Cytomics; 2002. Available from: http://isac.digiscript.com/presentation/index.cfm?media_id=8743
18. The DICOM standard, Rosslyn, VA: National Electrical Manufacturers Association; Official DICOM printed standard volumes. Available from: http://www.nema.org/index_nema.cfm/563/?type=standard&pageid= A314508D%2DA289%2D4D56%2D953C71DC9F7COD4E&node=694 [purchase] or http://medical.nema.org/dicom/2003.html [download]
19. Thompson HS, Beech D, Maloney M, Mendelsohn N. XML schema part 1: structures, W3C; 2001. Available from: www.w3.org/TR/2001/REC-xmlschema-1-20010502/
20. Biron PV, Malhotra A. XML schema part 2: datatypes, W3C; 2001. Available from: www.w3.org/TR/2001/REC-xmlschema-2-20010502/
21. Walmsley P. Definitive XML schema. Saddle Brook, NJ: Prentice-Hall; 2002.
22. IBM Corp. Leverage the power of XML in e-business applications, DB2 Universal Database XML Extender: Web-enabling your data with XML. Available from: http://www-3.ibm.com/software/data/db2/extenders/xmlext/xmlextfctsht.pdf
23. Microsoft Corp. Microsoft SQL server 2000 Web services toolkit. Availablr from: http://www.microsoft.com/sql/techinfo/xml/default.asp
24. Oracle Corp. Oracle XML developer's kits. Available from: http://otn.oracle.com/tech/xml/xdkhome.html
25. Software AG. Tamino XML server number one in XML management, white paper. Available from: http://www.softwareag.com/tamino/download/tamino.pdf
26. eXcelon Corp. eXtensible snformation server (XIS), native XML data management system. Available from: http://www.exln.com/products/xis/
27. Ipedo Corp. Products, Ipedo XML database. Available from: www.ipedo.com/html/
28. Work item proposal: DICOM Standard publication and maintenance in XML. Available from: http://medical.nema.org/dicom/minutes/wg-10/ahg-publish-xml/2003-02-27/ wg_10-workitemreq_dicominxml.doc
29. Brolund G. How to build an electronic common technical document. Washington, DC: US Food and Drug Administration, CDER/OIT. Available from: http://www.fda.gov/cder/present/dia72001/cderectdreview/ts1d001.htm
30. FDA/Center for Drug Evaluation and Research (CDER) proposed standard for exchange of electrocardiographic and other time-series data. Available from: http://www.fda.gov/cder/regulatory/ersr/ECGdata.htm
31. Brown B, Kohls M, Stockbridge N. Draft, FDA XML data format requirements specification, revision B. Available from: http://www. cdisc.org/discussions/EGC/ FDA_XML_Data_Format_Requirements_Specification_DRAFT_B.pdf
32. Brown B, Kohls M, Stockbridge N. Draft, FDA XML data format design specification, revision C. Available from: http://www.cdisc.org/discussions/EGC/ FDA%20_XML_Data_Format_Design_Specification_DRAFT_C.pdf
33. CMS ESRD. HL7 V3 XML specifications & design, end stage renal disease (ESRD). Washington, DC: US Department of Health and Human Services and Metaintegration Technology. Available from: http://www.metaintegration.net/CMS/
34. Future Eligibility Determination Systems. How standardization can help solve the challenges. Washington, DC: US Department of Health and Human Services. Available from: http://cms.hhs.gov/medicaid/eligibility/tanfdelink.pdf
35. Regenstrief Institute. LOINC and RELMA. Available from: http://www.loinc.org/download
36. Regenstrief Institute. LOINC database version LOINC 2.08. released September 13, 2002. Available from: http://www.loinc.org/download
37. Carlisle D, Ion P, Miner R, Poppelier N, editors. Mathematical markup language (MathML). Version 2.0. W3C recommendation; 21 February 2001. Available from: http://www.w3.org/TR/2001/REC-MathML220010221/
38. Schadow G, McDonald CJ. The unified code for units of measure (UCUM). Version 1.4. 27 April 2000. Regenstrief Institute for Health Care. Available from: http://aurora.rg.iupui.edu/UCUM/UCUM.pdf
39. SNOMED International, College of American Pathologists. Systematized nomenclature of medicine. SNOMED. Accessed 27 May 2002. Available from: http://www.snomed.org/
40. Digital Imaging and Communications in Medicine. PS 3.3-2003, A.34 waveform information object definitions and C.10.8 waveform identification module. Rosslyn, VA: National Electrical Manufacturers Association; 2003. Available from: http://medical.nema.org/dicom/2003/03_03PU.PDF
41. Leif RC, Leif SB, Leff SH. CytometryML, a markup language for analytical cytology. In: Enderlein J, Farkas DL, Leif RC, Nicolau DV, editors. Manipulation and analysis of biomolecules, cells, and tissues. Volume 4962. New York: SPIE Proceedings. Forthcoming.
42. Redelman D, Coder DM. Cell subset (CS) parameter to record the identities of individual cells in flow cytometric data. Cytometry 1994;18:95-102.
43. Digital Imaging and Communications in Medicine. Part 16: Content mapping resource, PS 3.16-2003, Table 8-1 coding schemes. Rosslyn, VA: National Electrical Manufacturers Association. Available from: http://medical.nema.org/dicom/2003/01-16PU.PDF
44. Digital Imaging and Communications in Medicine, Part 3: Information object definitions, PS 3.3-2003, Section C.7.6.3.1.2 Photometric Interpretation. Rosslyn, VA: National Electrical Manufactureres Association. Available from: http://medical.nema.org/dicom/2003/03_03PU.PDF
45. Digital Imaging and Communications in Medicine, Part 5: Data structures and encoding, PS 3.5-2003, Section 8.2 Native or encapsulated format encoding. Available from: http://medical.nema.org/dicom/2003/03_05PU.PDF
46. Dierks T, Allen C. The TLS protocol. Version 1.0. Response to network working group request for comments: 2246 category: standards track; 1999. Available from: http://www.rfc-editor.org/rfc/rfc2246.txt
47. Dierks T, Allen C. The TLS protocol. Version 1.0. Response to network working group request for comments: 2246 category: standards track; 1999. Available from: ftp://ftp/rfc-editor.org/in-notes/rfc2246.txt
48. W3C®, The technology & society domain, Technical building blocks that help address critical public policy issues on the Web. Available from: http://www.w3.org/TandS/