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Review of the ISAC Draft Requirements for a Cytometry /Analytical Cytology Data File Standard

Review of the ISAC Draft Requirements for a Cytometry /Analytical Cytology Data File Standard. Encode the required information to interpret a cytometry experiment Facilitate the reproduction of a cytometry experiment Efficiently store cytometry list mode data (Not relevant to image-based HCS)

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Review of the ISAC Draft Requirements for a Cytometry /Analytical Cytology Data File Standard

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  1. Review of the ISAC Draft Requirements for a Cytometry/Analytical Cytology Data File Standard

  2. Encode the required information to interpret a cytometry experiment • Facilitate the reproduction of a cytometry experiment • Efficiently store cytometry list mode data • (Not relevant to image-based HCS) • Transparently store text-based data • Facilitate support for other analytical cytology data

  3. Each type of information shall be uniquely identifiable • Use of Global Identifiers – need to add our own ontology for image-based, plate-based HCS • It shall be possible to resolve data files over the internet • Each type of information shall only be stored in one file format • As the core information in HCS is almost always image file data, does this mandate the use of a single image file format? Is this even workable for us?

  4. Support for future instruments • Can we envision a “future-proof” way of storing image data? • Provide semantic meaning to all required/standardized information • My interpretation – just means that everything in the standard is defined in a detailed fashion • Extensible by third parties • Could this possibly dilute the “standard” nature of the standard?

  5. Extensions shall be separated and removable from normative parts • Ensure that metadata can always be located • Implies either a “packaging” mechanism with internal links, or some kind of global metadata ID schema • Support for use cases where new metadata are being added subsequently • Is analysis just a form of metadata?

  6. Several instances of mutable information may share immutable information • You can perform & store multiple analyses or multiple interpretations of the same data • Some information may be encoded by a referenced semantic model or an existing standard • Use previously existing standards if applicable • Does this imply acceptance of any sufficiently “standard” image file format? • It shall be possible to refer to multiple semantic models or standards

  7. Use a manufacturer-independent format • Use a programming-language independent format • Use a file/operating system-independent format • Use a simple format oriented on data interoperability • Describe the standard unambiguously

  8. There shall be an open-review period before adopting the standard • There shall be a mechanism to formally validate the standard • The standard shall be public • An implementation of the standard shall be possible without charge • The implementation of the standard shall be non-restrictive • No licensing restrictions – any known or hidden IP traps here?

  9. Reuse existing standards • Cited examples: CEN, DICOM, HL7, W3C, etc. • Redundant? • Conformance to standards shall be (easily) testable • The file format shall be as self-explanatory as possible

  10. To obtain a copy of this document : Ryan Brinkman (brinkman@bccrc.ca) Kurt Scudder (kscudder@accelrys.com) D&IA SIG Website: http://www.ravkin.net/SBS/D&IA_SIG.htm Your comments are welcome! Please email to Ryan and/or Kurt

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