The Zebrafish Database Project
Specific Aim 2. WWW Graphical User Interface.
We will develop a set of tools for interacting with the
database via Internet. Our goal is to provide easy access to the database for
researchers with little or no knowledge of how the database operates. We also
want to make it possible for people everywhere to access the database over the
Internet using standard, inexpensive hardware and software. We presently favor
the use of a WWW browser like Mosaic or Netscape. We will design and build an interface to communicate with the database, initiating and receiving the
results of queries. The interface will pass this information back and forth to
the researchers through their local WWW clients using a series of forms. The
interface will also act as the arbitrator between the research labs and the
database ensuring uniformity of the data types and the assignment of proper
descriptors (attributes) to data records, thus enforcing a data model.
Researchers will use forms to interact with the database. To submit image data,
the scientist would first transfer the image (e.g. via ftp) to a temporary file
on the server. Then, after providing the name of the file and appropriate
password and account information, various attributes of the data record would
be chosen from pre-determined lists. For example, to submit the image shown in Fig 1, the form would be filled out as shown below, specifying that
it is a whole-mount stained with the HNK-1 antibody, labeling cells of the
diencephalon, etc.
After the attributes are checked by the user interface
program to make sure that they conform to the data model, the image would be
entered into the database. To search for particular data records, a query would
be initiated using a form as illustrated in the form below.
Various data attributes
could be combined to make a complex query. For example, Development AND Morphology AND Probes could be selected to bring up the Image viewing tool shown below. By filling in the form with specific attributes like HNK-1, Diencephalon, etc., the record shown in the form below would be retrieved.
Additional tools will be developed for submitting and viewing the other data
types.
This type of database querying is novel because it is based on
graphical/spatial information within an image. Nevertheless, several groups are
starting to develop methods for integrating images into biological databases
[Fox94]. The Jackson Lab is coordinating the design of a database for mouse which will include 3D reconstructions and links to gene expression patterns [Ringwald94]. With these people as consultants we can build upon the tools they have already developed and ensure semantic compatibility of zebrafish data with those from other species [Robbins94,Fox94].
The Zebrafish Database
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