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ACS – the Archival Cytometry Standard

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ACS – the Archival Cytometry Standard http://flowcyt.sf.net/acs/latest.pdf ACS – the Archival Cytometry Standard Archival Cytometry Standard ACS International Society for Advancement of Cytometry Candidate Recommendation DRAFT Document Status The Archival Cytometry Standard (ACS) has undergone several revisions since its initial development in June 2007. The current proposal is an ISAC Candidate Recommendation Draft. It is assumed, however not guaranteed, that significant features and design aspects will remain unchanged for the final version of the Recommendation. This specification has been formally tested to comply with the W3C XML schema version 1.0 specification but no position is taken with respect to whether a particular software implementing this specification performs according to medical or other valid regulations. The work may be used under the terms of the Creative Commons Attribution-ShareAlike 3.0 Unported license. You are free to share (copy, distribute and transmit), and adapt the work under the conditions specified at http://creativecommons.org/licenses/by-sa/3.0/legalcode. Disclaimer of Liability The International Society for Advancement of Cytometry (ISAC) disclaims liability for any injury, harm, or other damage of any nature whatsoever, to persons or property, whether direct, indirect, consequential or compensatory, directly or indirectly resulting from publication, use of, or reliance on this Specification, and users of this Specification, as a condition of use, forever release ISAC from such liability and waive all claims against ISAC that may in any manner arise out of such liability. ISAC further disclaims all warranties, whether express, implied or statutory, and makes no assurances as to the accuracy or completeness of any information published in the Specification. In issuing and making this Specification available, ISAC is not undertaking to render professional or other services for or on behalf of any person or entity, nor is ISAC undertaking to perform any duty owed by any person or entity to someone else. Anyone using this document should rely on his or her own independent judgment or, as appropriate, seek the advice of a competent professional in determining the exercise of reasonable care in any given circumstances. Attention is called to the possibility that implementation of this Specification may require use of subject matter covered by patent rights. By publication of this standard, no position is taken with respect to the existence or validity of any patent rights in connection therewith. ISAC shall not be responsible for identifying patents or patent applications for which a license may be required to implement an ISAC standard or for conducting inquiries into the legal validity or scope of those patents that are brought to its attention. ACS 1.0, DRAFT of ISAC Candidate Recommendation, version 150428, April 28, 2015 Version 1.0, 150428 Warning: This is a Draft of an ISAC Candidate Recommendation i http://flowcyt.sf.net/acs/latest.pdf ACS – the Archival Cytometry Standard Abstract The Flow Cytometry Standard (FCS) specification has been adopted for the common representation of flow cytometry data, and this standard is supported by all analytical instrument and third party software vendors. It includes data and metadata describing the subject being analyzed as well as the acquisition conditions. There are several use cases requiring these raw FCS files to remain intact after the data have been collected. However, since data analysis is typically performed post-acquisition, it is commonly stored in additional files, such as proprietary project files and workspaces, or standard Gating-ML files. This practice introduces the need of being able to bundle data with related additional information. This document represents the Archival Cytometry Standard (ACS), which has been developed to bundle data with different components describing cytometry experiments. It captures relations among data and other components and includes support for audit trails, versioning and digital signatures. The ACS container is based on the ZIP file format with an XML-based Table of Contents specifying relations among files in the container. The XML Signature W3C Recommendation has been adopted to allow for digital signatures of data and other components within the ACS container. Keywords: flow cytometry, cytology, data standard, file format, FCS, ZIP, XML Version 1.0, 150428 Warning: This is a Draft of an ISAC Candidate Recommendation ii http://flowcyt.sf.net/acs/latest.pdf ACS – the Archival Cytometry Standard TABLE OF CONTENTS 1. Overview .................................................................................................................................................... 1 1.1 Introduction ......................................................................................................................................... 1 1.2 Scope ................................................................................................................................................... 1 1.3 Purpose ................................................................................................................................................ 1 1.4 Normative References ......................................................................................................................... 2 1.5 The Content of this Specification ........................................................................................................ 2 1.6 Acronyms and Abbreviations .............................................................................................................. 2 1.7 Keywords Indicating Requirement Levels ........................................................................................... 3 1.8 Namespaces and their Prefixes within this Document ......................................................................... 3 2. Design Principles and Rationale ................................................................................................................. 3 2.1 Using ZIP as the Container File Format .............................................................................................. 3 2.2 Using XML for Container’s Table of Contents ................................................................................... 4 2.3 Using W3C XML Signatures for Digital Signatures of ACS Components ......................................... 5 3. Conformance .............................................................................................................................................. 5 3.1 File Conformance ................................................................................................................................ 5 3.2 Software and Hardware Conformance ................................................................................................. 6 4. General ....................................................................................................................................................... 6 4.1 ACS File Name .................................................................................................................................... 6 4.2 ACS File Format .................................................................................................................................. 6 4.3 Naming Files and Directories within the ACS Container .................................................................... 6 4.4 ACS Contents and Audit Trail ............................................................................................................. 7 4.4.1 ACS Table of Contents ................................................................................................................ 7 4.4.2 Other Files in ACS ....................................................................................................................... 7 4.4.3 Audit Trail Implementation ......................................................................................................... 7 5. ACS Table of Contents Format .................................................................................................................. 8 5.1 General ................................................................................................................................................ 8 5.2 Table of Contents File Structure .......................................................................................................... 8 5.3 Parent Table of Contents ..................................................................................................................... 9 5.4 Listing Files in ACS Table of Contents ............................................................................................. 10 5.4.1 File Resource Identifiers ............................................................................................................ 10 5.4.2 File Types .................................................................................................................................. 10 5.4.3 Free Text File Description ......................................................................................................... 11 5.5 Associations Between Files ............................................................................................................... 11 5.6 Additional Information in the Table of Contents ............................................................................... 12 5.7 Digital Signatures .............................................................................................................................
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