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FCS 4.0 – The Analytical Cytometry Standard, By John Quinn Ph.D. Work is underway in developing the next flow cytometry standard file format. The working name for this file won’t be FCS 4.0, but the Analytical Cytometry Standard, or ACS. The shift in naming convention is meant to convey a major shift in the format of data storage. Previous versions of fcs incorporated all of the data and metadata into a single file with an FCS header. ACS will actually be a container file that will house a number of sub-files of different formats each selected to house a particular portion of the data. Lets begin with an illustration of the proposed format. As shown in the picture, the ACS container itself would be a compressed file, such as a .zip file, to allow for smaller storage and transport size. The data itself would be stored as a binary matrix following the netCDF standard, and stripped of the metadata. Using this format would allow for efficient use of memory, easy parsing, much greater ease in accessing flow data through other software. Data mining tools are an excellent use case for accessing the raw data. The metadata would of course still be stored, but stored in a set of XML files, divided up by MIFlowCyt defined subsets. RDF, Resource Definition Framework, file types are being considered as an option to XML. The advantage of RDF would be that it is a form of XML that allows for structure to be imparted to the meta data through the use of “triples”, sentence like constructs with RDF that convey meaning to metadata, and that RDF is a format that computers can garner meaning from through the triples. Because computers can take meaning from the data, machines can be used to perform automated routines, such as searching, parsing or data entry. For more information on RDF, the w3c website is an excellent resource: http://www.w3.org/TR/REC-rdf-syntax/. The ACS container is also proposed to contain gating, transformation, and compensation XML documents that are intended to retain some of the data analysis This format is still some time away from being implemented, but tools to ease the transition to this new format are in progress now. One example is the creation of a flow cytometry ontology, a controlled language defining flow terms. One subset of this ontology is the instrumentation ontology and in this file we are building a definition of all cytometers, with the goal of being able to export the MIFlowCyt suggested information from the ontology into an XML format, essentially producing a portion of the ACS container. We’ll revisit this issue in greater detail in a future MyCyte article. For more on this topic, contact John Quinn, Ph.D. John Quinn, Ph.D. Application Scientist Tree Star, Inc. www.flowjo.com john@treestar.com |
