With ACS containers we need to have some kind of container index format that makes the link between the list mode data file(s) (FCS or netCDF) and the gating file(s), as well as any additional metadata that may be present.
A recent trend in data standard development has been to use Extensible Markup Language (XML) as the preferred mechanism to define data representations. We suggest using XML where appropriate based on the character of stored information, as exemplified by the proposed Gating-ML. However, the syntactic and document-centric XML cannot achieve the level of interoperability required for highly dynamic metadata, such as FCM experiment annotation.
RDF enables encoding, exchange and reuse of structured metadata. It is an application of XML that imposes needed structural constraints to provide unambiguous methods of expressing semantics. Moreover, it provides means for publishing both human-readable and machine-processable vocabularies designed to encourage the reuse and extension of metadata among disparate information communities.
Within the flowRDF document we demonstrate how to reuse standardized RDF metadata elements (defined by resource description communities, e.g., the Dublin Core Metadata Initiative), how to create and reference FCM specific metadata elements, and how to use biological ontologies to annotate FCM data.
The latest version of the flowRDF document may be downloaded from: http://flowcyt.sourceforge.net/flowrdf/latest.pdf.