The OMERO.editor screen layout
OMERO.editor is an editing tool for scientists to record and manage their experimental metadata.
This tool is a stand-alone application, but will soon become integreated with other OMERO software, such that this metadata may be used to annotate images in OMERO.
OMERO.editor is a Java tool, that can be downloaded, along with some example files, from http://users.openmicroscopy.org.uk/~will/
Experimental metadata is represented within OMERO.editor in the form of fields, which can be arranged hierarchically (see figure).
A number of fields can be used to describe a protocol or data model, by editing the field name and adding a description to each field. In addition, a field may be used to record an experimental variable, or frequently changing parameter, such as the time, number, date etc.
The workspace of the editor displays the layout of the hierarchical fields in the larger left-hand panel. The variable parameters of each field can be edited here, and the hierarchy can be browsed by expanding or collapsing different levels of the tree.
The data model template can be edited using the toolbar and panel to the right. The field name, description and other details can be edited when a particular field is highlighted. Furthermore, fields can be added, duplicated, deleted, rearranged, copied, pasted and imported using the template-editing toolbar to the right.
OMERO.editor can incorporate pre-defined schemas and ontologies in a number of ways.
Data in the form of XML files can be edited or imported into OMERO.editor documents, allowing the re-use of existing data models. For example, the figure describes a microarray experiment, in which the microarray design is specifed by MAGE-ML, the XML language of the MAGE project. The MAGE-ML document to be imported is displayed on the right, where fields can be selected for import. In this case, the whole document has been imported into the current protocol (left panel). Attributes for each XML element can be edited by clicking on the note-pad icon (as shown for the OntologyEntry element).
OMERO.editor also supports the use of terms from the Open Biomedical Ontologies (OBO). These can be accessed via auto-complete fields, providing a convenient way of using pre-defined terms to create your own data model. In this screen-shot, a movie of dividing cells is being described using several terms from the GO and PATO ontologies to define a phenotype.
OMERO.editor files can be indexed and then searched using two methods. A keyword "Google-like" search can be performed using the search-box at the top-right of the screen. Alternatively, it is possible to search for files that are similar to the currently opened file, using the "More-Like-This" search button, as shown in the figure below. Search results are displayed and the corresponding files can then be opened. In this screen-shot, the current file is a protocol for fixing and staining cells, a proceedure that has been copied into a number of other experiments. These experiments have been identified using a More-Like-This search.
