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Figure 1 | BMC Bioinformatics

Figure 1

From: FuGEFlow: data model and markup language for flow cytometry

Figure 1

Extending FuGE classes to model Sample, Organism, and Fluorescent Reagent. Figure 1A shows FuGE classes in light brown and Flow-OM classes in bright yellow. The Organism class exemplifies a non FCM-specific concept common across a wide range of biological domains. Organism inherits identification and other generic properties, as well as the ability to be consumed and produced in a protocol application, from the FuGE Material class. Organism properties defined in the MIFlowCyt, such as taxonomy, gender, and age are modelled explicitly as references to the OntologyTerm, Description and AtomicValue classes. ExternalData is used to reference files outside of the scope of the model, in this case phenotype and genotype files of the Organism. The FluorescentReagent class is an example of a composite biological material. FluorescentReagent combines reporter (GenericMaterial), detector (AnalyteDetector) and a list of analytes (GenericMaterial) into a single biological material. Figure 1B shows the corresponding Flow-ML representation of a fluorescent reagent. In FCM experiments a fluorescent reagent usually consists of an analyte detector (antibody) and a reporter (fluorescence marker). An analyte detector is a common entity in various biological experiments and is described by the analytes (antigens) it binds to. In this example, reagent CD4_TxRed consists of the reporter TxRed and the analyte detector anti-CD4. The analyte detector anti-CD4 binds with the analyte CD4.

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