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Submitting 3D patterns into the Database
To submit 3D patterns of gene expression, submitters need an account to start a submission process. New members from the bio-imaging group are able to register online for an account. They can use the registration form. Users outside the bio-imaging group have to contact the webmaster for an account.
Information submission to GEMS consists of 3D multi-channel CLSM images and the patterns of gene expression in these images. These images are annotated using concepts from two domain ontologies i.e. the Developmental Anatomy Ontology Of Zebrafish (DAOZ) and the Gene Ontology (GO; http://geneontology.org). The DAOZ is used to describe the spatial, temporal and functional characteristics of the expression. The GO is used to annotate patterns of gene expression in the images with gene information. Furthermore, the 3D images annotation is completed by experimental conditions and extra probe information. For this information, special forms have to be filled and sent to the system database. The system guides the user though this forms before getting into an upload page. In this page the user has to specify the right developmental stage, location and functional system of the expression field. The system uses these variables to generate a query and submit it to the DAOZ database (our anatomical ontology) to generate a list of anatomical structures. From this list, the user needs then, to select the right anatomical names of the expression field. To complete the submission process, in the upload page extra fields have to be filled and the right path of the 3D image has to be specified. Optionally imaging conditions could be uploaded (Usually it is generated by the CLSM in the form of an XML file).
Viewing images in the Database
Searching the system is a free service. Users do not need access authentication to search the system. They can perform a quick as well as an advanced search. Both search options could be reached through the search link.
- Search results are in the form of a set of thumbnail images.
- Each image is titled with its stage of development.
- Each image could be clicked to view it in a larger size and to get more details about the used probe, experimental conditions, location and functional system of the expression field.
- Links to relevant information into other database systems are also provided.
Last modified: November 2010.