CytometryML, an XML format based on DICOM and FCS for analytical cytology data

• Published in: Cytometry. Part A Vol. 54A; no. 1; pp. 56 - 65
• Main Authors: Leif, Robert C., Leif, Suzanne B., Leif, Stephanie H.
• Format: Journal Article
• Language: English
• Published: Hoboken Wiley Subscription Services, Inc., A Wiley Company 01.07.2003
• Subjects: Computer Communication Networks - standards; Cytometry Markup Language (Cytometry ML); Digital Imaging and Communications in Medicine (DICOM); Extensible Markup Language (XML); Feasibility Studies; Flow Cytometry - standards; Flow Cytometry Standard (FCS); Humans; Information Systems - standards; Programming Languages; schema; Software; waveform
• ISSN: 1552-4922; 1552-4930; 1552-4930
• DOI: 10.1002/cyto.a.10043

Background Flow Cytometry Standard (FCS) was initially created to standardize the software researchers use to analyze, transmit, and store data produced by flow cytometers and sorters. Because of the clinical utility of flow cytometry, it is necessary to have a standard consistent with the requirements of medical regulatory agencies. Methods We extended the existing mapping of FCS to the Digital Imaging and Communications in Medicine (DICOM) standard to include list‐mode data produced by flow cytometry, laser scanning cytometry, and microscopic image cytometry. FCS list‐mode was mapped to the DICOM Waveform Information Object. We created a collection of Extensible Markup Language (XML) schemas to express the DICOM analytical cytologic text‐based data types except for large binary objects. We also developed a cytometry markup language, CytometryML, in an open environment subject to continuous peer review. Results The feasibility of expressing the data contained in FCS, including list‐mode in DICOM, was demonstrated; and a preliminary mapping for list‐mode data in the form of XML schemas and documents was completed. DICOM permitted the creation of indices that can be used to rapidly locate in a list‐mode file the cells that are members of a subset. DICOM and its coding schemes for other medical standards can be represented by XML schemas, which can be combined with other relevant XML applications, such as Mathematical Markup Language (MathML). Conclusions The use of XML format based on DICOM for analytical cytology met most of the previously specified requirements and appears capable of meeting the others; therefore, the present FCS should be retired and replaced by an open, XML‐based, standard CytometryML. Cytometry Part A 54A:56–65, 2003. © 2003 Wiley‐Liss, Inc.