title: Metadata management for high content screening in OMERO.
abstract: High content screening (HCS) experiments create a classic data management challenge-multiple, large sets of heterogeneous structured and unstructured data, that must be integrated and linked to produce a set of "final" results. These different data include images, reagents, protocols, analytic output, and phenotypes, all of which must be stored, linked and made accessible for users, scientists, collaborators and where appropriate the wider community. The OME Consortium has built several open source tools for managing, linking and sharing these different types of data. The OME Data Model is a metadata specification that supports the image data and metadata recorded in HCS experiments. Bio-Formats is a Java library that reads recorded image data and metadata and includes support for several HCS screening systems. OMERO is an enterprise data management application that integrates image data, experimental and analytic metadata and makes them accessible for visualization, mining, sharing and downstream analysis. We discuss how Bio-Formats and OMERO handle these different data types, and how they can be used to integrate, link and share HCS experiments in facilities and public data repositories. OME specifications and software are open source and are available at https://www.openmicroscopy.org.
authors.affiliation: Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK.
authors.forename: Simon
authors.initials: S
authors.lastname: Li
authors.affiliation: Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK.
authors.forename: Sébastien
authors.initials: S
authors.lastname: Besson
authors.affiliation: Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK.
authors.forename: Colin
authors.initials: C
authors.lastname: Blackburn
authors.affiliation: Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK.
authors.forename: Mark
authors.initials: M
authors.lastname: Carroll
authors.affiliation: Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK.
authors.forename: Richard K
authors.initials: RK
authors.lastname: Ferguson
authors.affiliation: Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK.
authors.forename: Helen
authors.initials: H
authors.lastname: Flynn
authors.affiliation: Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK.
authors.forename: Kenneth
authors.initials: K
authors.lastname: Gillen
authors.affiliation: Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK.
authors.forename: Roger
authors.initials: R
authors.lastname: Leigh
authors.affiliation: Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK.
authors.forename: Dominik
authors.initials: D
authors.lastname: Lindner
authors.affiliation: Glencoe Software, Inc., Seattle, WA, USA.
authors.forename: Melissa
authors.initials: M
authors.lastname: Linkert
authors.affiliation: Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK.
authors.forename: William J
authors.initials: WJ
authors.lastname: Moore
authors.affiliation: Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK.
authors.forename: Balaji
authors.initials: B
authors.lastname: Ramalingam
authors.affiliation: Glencoe Software, Inc., Seattle, WA, USA.
authors.forename: Emil
authors.initials: E
authors.lastname: Rozbicki
authors.affiliation: Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK.
authors.forename: Gabriella
authors.initials: G
authors.lastname: Rustici
authors.affiliation: Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK.
authors.forename: Aleksandra
authors.initials: A
authors.lastname: Tarkowska
authors.affiliation: Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK.
authors.forename: Petr
authors.initials: P
authors.lastname: Walczysko
authors.affiliation: Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK.
authors.forename: Eleanor
authors.initials: E
authors.lastname: Williams
authors.affiliation: Glencoe Software, Inc., Seattle, WA, USA.
authors.forename: Chris
authors.initials: C
authors.lastname: Allan
authors.affiliation: Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK.
authors.forename: Jean-Marie
authors.initials: JM
authors.lastname: Burel
authors.affiliation: Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK; Glencoe Software, Inc., Seattle, WA, USA.
authors.forename: Josh
authors.initials: J
authors.lastname: Moore
authors.affiliation: Centre for Gene Regulation & Expression, University of Dundee, Dundee, Scotland, UK; Glencoe Software, Inc., Seattle, WA, USA. Electronic address: jrswedlow@dundee.ac.uk.
authors.forename: Jason R
authors.initials: JR
authors.lastname: Swedlow
mesh_terms: D019295:Computational Biology / Q000379:methods / Q000706:statistics & numerical data*; D057225:Data Mining / Q000706:statistics & numerical data*; D066264:Datasets as Topic; D057166:High-Throughput Screening Assays / Q000379:methods / Q000706:statistics & numerical data*; D006801:Humans; D033181:Information Dissemination; D016247:Information Storage and Retrieval / Q000379:methods / Q000706:statistics & numerical data*; D020407:Internet; D012984:Software
keywords: Data management; HCS; Metadata; Screening