The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging

I. Goldberg; Chris Allan; Jean‐Marie Burel; Doug Creager; Andrea Falconi; Harry Hochheiser; Josiah Johnston; Jeff Mellen; Peter K. Sorger; Jason R. Swedlow

doi:10.1186/gb-2005-6-5-r47

Abstract

Abstract The Open Microscopy Environment (OME) defines a data model and a software implementation to serve as an informatics framework for imaging in biological microscopy experiments, including representation of acquisition parameters, annotations and image analysis results. OME is designed to support high-content cell-based screening as well as traditional image analysis applications. The OME Data Model, expressed in Extensible Markup Language (XML) and realized in a traditional database, is both extensible and self-describing, allowing it to meet emerging imaging and analysis needs.

Keywords

XMLComputer scienceMarkup languageInformaticsSoftwareFile formatXML frameworkMicroscopyExtensibilityDatabaseWorld Wide WebProgramming languagePathologyEngineering

Affiliated Institutions

Related Publications

Chemical Markup, XML, and the Worldwide Web. 1. Basic Principles

Peter Murray‐Rust , Henry S. Rzepa

Chemical markup language (CML) is an application of XML, the extensible markup language, developed for containing chemical information components within documents. Its design su...

1999 Journal of Chemical Information and C... 228 citations

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

Remco Bouckaert , Joseph Heled , Denise Kühnert +6 more

We present a new open source, extensible and flexible software platform for Bayesian evolutionary analysis called BEAST 2. This software platform is a re-design of the popular B...

2014 PLoS Computational Biology 6674 citations

jmz<scp>I</scp>dent<scp>ML API</scp>: A <scp>J</scp>ava interface to the mz<scp>I</scp>dent<scp>ML</scp> standard for peptide and protein identification data

Florian Reisinger , Ritesh Krishna , Fawaz Ghali +4 more

We present a J ava application programming interface ( API ), jmz I dent ML , for the Human Proteome Organisation ( HUPO ) Proteomics Standards Initiative ( PSI ) mz I dent ML s...

2012 PROTEOMICS 28 citations

jmzTab: A Java interface to the mzTab data standard

Qingwei Xu , Johannes Griss , Rui Wang +3 more

mzTab is the most recent standard format developed by the Proteomics Standards Initiative. mzTab is a flexible tab‐delimited file that can capture identification and quantificat...

2014 PROTEOMICS 16 citations

XML–Based Schema Definition for Support of Interorganizational Workflow

Wil M. P. van der Aalst , Akhil Kumar

The full potential of the Web as a medium for electronic commerce can be realized only when multiple partners in a supply chain can route information among themselves in a seaml...

2003 Information Systems Research 200 citations

Publication Info

Year: 2005
Type: article
Volume: 6
Issue: 5
Pages: R47-R47
Citations: 313
Access: Closed

External Links

View on DOI.org

Social Impact

Altmetric

The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging

PlumX Metrics

Social media, news, blog, policy document mentions

Citation Metrics

313

OpenAlex

Cite This

APA Style

                            
                                
                                    I. Goldberg, 
                                
                                    Chris Allan, 
                                
                                    Jean‐Marie Burel
                                
                                et al.
                            
                            (2005). 
                            The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging. 
                            Genome biology
                            , 6
                            (5)
                            , R47-R47.
                            https://doi.org/10.1186/gb-2005-6-5-r47
                        

Identifiers

DOI: 10.1186/gb-2005-6-5-r47