Purpose: The goal of the Zebrafish Reference Resource (ZERR) is to provide researchers with a comprehensive and uniform reference framework for (a) naming and identifying anatomical features of the zebrafish and (b) naming and identifying the various developmental stages. In particular, four distinct reference facilities are embodied in the ZERR:
1) The Staging Series. The purpose of the staging series is to establish a common framework for identifying the developmental stage of an animal. Each of the developmental stages currently agreed upon by the zebrafish research community is textually described and extensively documented with carefully selected photographic records that exemplify the stage in question.
Usage Scenario: I have a photo of an interesting fish, but I’m unsure what its stage is. So I browse through the Staging Series, referring to the criteria and images found there to determine the stage of my specimen.
2) The Developmental Atlas. The developmental atlas (when completed) provides a comprehensive visual atlas of the zebrafish providing, for each developmental stage, a set of whole-mount and section images. Most of these images will be annotated to identify various anatomical structures. The goal of the atlas is to allow researchers to identify the anatomical structures observed in their own specimens.
Usage Scenario: I am looking at a labeled cross-section showing some gene expression pattern and am unsure of a particular structure that is labeled. So I search the Anatomical Atlas for an annotated image of that region and am able to determine the correct anatomical term for the structure.
3) Adult Atlas. The Adult Atlas is a subset of the developmental atlas that focuses narrowly on the anatomical structure of the adult (older than 3 months) zebrafish. Like the developmental atlas, it indexes annotated whole-mounts and sections. Used in a way very similar to the Developmental Atlas.
4) Anatomical Parts Catalog. The purpose of the anatomical parts catalog is to define a stable, shared taxonomy of zebrafish anatomy, providing researchers with a common terminology for identifying the various anatomical structures in the zebrafish. In this way, the parts catalog reduces the confusion associated with synonymous terms for the same structure. The anatomical parts catalog is used to identify structures apparent in image data submitted to the database, thus enforcing the uniform terminology.
Usage Scenario: A colleague has sent me email mentioning that she has just documented expression of a gene in the pectoral fin buds. I can’t recall exactly where those structures are, at what stages they are present, or what they look like. I access the database to view a variety of annotated images of that structure (even including, perhaps, the very images that my colleague was speaking of, which she has promptly submitted to the database).
As shown in the figure, the ZERR establishes a comprehensive, shared framework for identifying and discussing aspects of zebrafish anatomy and development at all stages in the developmental process. For each stage, the database user has access to the criteria defining that stage (the Staging Series), to a comprehensive, annotated, and detailed visual catalog of zebrafish anatomy at that stage (the Developmental/Adult atlas), and to a detailed, cross-referenced definition of anatomical taxonomy at that stage (the Anatomical Parts list).
Unlike most other parts of the database, which generally require several new data categories to implement, the ZERR requires only two. This is because the ZERR can be seen primarily as an interface to data of types that already exist. Specifically, most of the reference data consist of images and their accompanying descriptions, which are already supported by the IMAGE data type. Implementing the ZERR is primarily a matter of providing interface mechanisms that allow users to extract and examine the appropriate image data. Two new data classes must be established to represent, respectively, the various anatomical parts and the hierarchical structural relationships among them.
Note the similarity among the Adult Atlas, the Staging Series, the Developmental Atlas, the Anatomical Parts and the Image data type. All are based on images that users need to constrain and browse. This suggests a common interface should be used to access all of them.