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. 2008 Dec;73A(12):1151-7.
doi: 10.1002/cyto.a.20637.

Gating-ML: XML-based Gating Descriptions in Flow Cytometry

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Free PMC article

Gating-ML: XML-based Gating Descriptions in Flow Cytometry

Josef Spidlen et al. Cytometry A. .
Free PMC article

Abstract

The lack of software interoperability with respect to gating due to lack of a standardized mechanism for data exchange has traditionally been a bottleneck, preventing reproducibility of flow cytometry (FCM) data analysis and the usage of multiple analytical tools. To facilitate interoperability among FCM data analysis tools, members of the International Society for the Advancement of Cytometry (ISAC) Data Standards Task Force (DSTF) have developed an XML-based mechanism to formally describe gates (Gating-ML). Gating-ML, an open specification for encoding gating, data transformations and compensation, has been adopted by the ISAC DSTF as a Candidate Recommendation. Gating-ML can facilitate exchange of gating descriptions the same way that FCS facilitated for exchange of raw FCM data. Its adoption will open new collaborative opportunities as well as possibilities for advanced analyses and methods development. The ISAC DSTF is satisfied that the standard addresses the requirements for a gating exchange standard.

Conflict of interest statement

Authors’ Disclosures of Potential Conflicts of Interest

Authors have no conflicts of interest.

Figures

Figure 1
Figure 1. Gate types supported by Gating-ML
Overview of the 6 types of gates supported by Gating-ML: rectangular gates in an arbitrary number of dimensions, i.e., going from 1-dimensional range gates up to multidimensional hypercube gates; polygon gates, ellipsoid and hyper-ellipsoid gates, polytope gates, decision tree structures, and Boolean collections of any of the types of gates.
Figure 2
Figure 2. Gating-ML description of gates
Examples of XML fragments demonstrating description of each of the types of gates. The XML structure is defined by Gating-ML XML schema and few additional validity requirements as specified in the Gating-ML normative description. Due to space constrains, examples have been simplified in that neither full XML nor fully qualified names (distribution into separate namespaces) are shown. Please consult examples included as supplementary material for distribution into separate namespaces for gating, transformation, and others.

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