Open Microscopy Environment Schemas

Table of contents

1. Introduction
2. History
3. Schemas

Introduction

This document outlines the XML Schemas created by the Open Microscopy Environment Group. Detailed information on the schemas and future development plans are available at http://www.openmicroscopy.org/site/support/file-formats. Further information on the groups work is available at http://www.openmicroscopy.org/

Auto generated documentation for the schemas is is available on the development server: http://git.openmicroscopy.org/src/develop/components/specification/Documentation/Generated/OME-2011-06/ome.html and http://git.openmicroscopy.org/src/develop/components/specification/Documentation/Generated/OME-2011-06/OMERO.html

History

This lists the past schemas. The schemas are in a process of constant development to extend and refine the OME Data Model.

• June 2007 - Major release - new namespace /2007-06/
• September 2007 - Minor release - version number increment
• February 2008 - Major release - new namespace /2008-02/
• May 2008 - Minor release - version number increment
• September 2008 - Major release - new namespace /2008-09/
• September 2009 - Major release - new namespace /2009-09/
• April 2010 - Major release - new namespace /2010-04/
• June 2010 - Major release - new namespace /2010-06/
• June 2011 - Major release - new namespace /2011-06/

For information on the schemas released before June 2007 is available at http://www.openmicroscopy.org/XMLschemas/. This includes the schemas used by the original OME server.

Schemas

This has the schema name, the current version, a link to the XSD file, and a short description

Note: Some browsers will try to render XSD files when you view them. This can result in either a blank screen or unformatted text. Choose to either download the file or view the source.

Active Schemas

• BinaryFile - June 2011 Version 1 [BinaryFile.xsd] The Binary File schema is used to describes a file location, or the location of a fragment within a file.
• OME - June 2011 Version 1 [ome.xsd] The main schema which defines the OME ontology for microscopy. This schema makes use of the others.
• OMERO - June 2011 Version 1 [OMERO.xsd] The schema extensions used by OMERO. It is not used by the OME schema but provides a structure for data in StructuredAnnotation blocks used by OMERO.
• ROI - June 2011 Version 1 [ROI.xsd] The Region Of Interest schema.
• SA - June 2011 Version 1 [SA.xsd] The Structured Annotation schema.
• SPW - June 2011 Version 1 [SPW.xsd] The Screen/Plate/Well schema.

Legacy Schemas

• AnalysisChain - September 2009 Version 1 [AnalysisChain.xsd] The Analysis Chain schema. Analysis chains are how module outputs are connected to inputs of other modules.
• AnalysisModule - September 2009 Version 1 [AnalysisModule.xsd] The Analysis Module Library schema. Analysis modules are image analysis algorithms or, more generally, how information is generated in OME. Makes use of CLI and MLI schemas.
• CA - September 2009 Version 1 [CA.xsd] The standard custom attribute schema.
• CLI - September 2009 Version 1 [CLI.xsd] The Command Line Interface sub-schema.
• DataHistory - September 2009 Version 1 [DataHistory.xsd] The Data History schema. Data history describes the data dependency in OME.
• MLI - September 2009 Version 1 [MLI.xsd] The Matlab Interface sub-schema.
• STD - September 2009 Version 1 [STD.xsd] The Semantic Type definition schema. Once a Semantic Type is defined, data for the defined type can be imported into the OME server.