ZFIN
The Zebrafish Model Organism Database
Funded by the National Human Genome Research
Institute (P41 HG002659) of the National
Institutes
of Health
Background:
A group of us were appointed at the 1994 Cold Spring
Harbor meeting on zebrafish genetics and development,
to establish an on-line database of information
for
zebrafish researchers.
Goals:
ZFIN serves as the zebrafish model organism database.
The long term goals for ZFIN are a) to be the
community database resource for the laboratory use
of zebrafish, b) to develop and support integrated
zebrafish genetic, genomic and developmental information,
c) to maintain the definitive reference data sets
of zebrafish research information, d) to link this
information extensively to corresponding data in other
model organism and human databases, e) to facilitate
the use of zebrafish as a model for human biology
and f) to serve the needs of the research community.
ZIRC is the Zebrafish International Resource Center, an independent NIH-funded facility providing a wide range of zebrafish lines, probes and health services. ZFIN works closely with ZIRC to connect our genetic data with available probes and fish lines.
Research staff:
Monte Westerfield, P.I.;
Judy Sprague, database director;
and the rest of the
ZFIN
Database Team.
Advisory board:
Janan T. Eppig, Jackson Laboratory;
William Gelbart, Harvard University; Tim Hubbard, Sanger Institute of the Wellcome Trust; Stephen Johnson,
Washington University; Robert Geisler, Max Planck
Institut, Tübingen; Teresa Nicolson, Oregon Health & Science University.
Publications:
- Sprague, J., Bayraktaroglu, L., Clements, D., Conlin, T., Fashena, D., Frazer, K., Haendel, M., Howe, D.G., Mani, P., Ramachandran, S., Schaper, K., Segerdell, E., Song, P., Sprunger, B., Taylor, S., Van Slyke, C.E., and Westerfield, M. (2006). The Zebrafish Information Network: the zebrafish model organism database.
- The
ZFIN database design document
describes the relational database implementation used in
ZFIN. It discusses both the model that is in production, as
well as work that is currently in development. The
original proposed
data model, dating from 1997, is also available online.
- Judy Sprague, Eckehard
Doerry, Sarah Douglas and Monte Westerfield. (2001).
The Zebrafish Information Network (ZFIN): a resource
for genetic, genomic and developmental research.
Nucleic Acid Res. 29:87-90.
- Westerfield,
M., Doerry, E., and Douglas, S. (1999) Zebrafish
in the net. Trends Genet. 15(6):248-249. This
manuscript describes the history of the ZFIN database
project.
- Monte
Westerfield, Eckehard Doerry, Arthur E. Kirkpatrick
and Sarah A. Douglas. (1999). Zebrafish informatics
and the ZFIN database. Meth. Cell Biol. 60:339-355.
This paper describes the data model and structure
of the database.
- Edwards,
P. (1999) Zebrafish Web Site Listings. In The Zebrafish:
Genetics and Genomics, H.W. Detrich, III, M. Westerfield,
and L.I. Zon, eds., San Diego: Academic Press, Meth.
Cell Biol. 60:373-385.
- Eckehard Doerry, Monte Westerfield, Sarah A.
Douglas and Arthur E. Kirkpatrick. (1998). The zebrafish
information network project. ACM Interactions 3:69.
This report describes our design process.
- Eckehard Doerry, Sarah A. Douglas, Arthur E.
Kirkpatrick, Monte Westerfield. 1997. Moving
beyond HTML to Create a Multimedia Database with
User-Centered Design: A Case Study of a Biological
Database. Tech. Report CIS-TR-97-02, Computer
and Information Science Dept., University of Oregon.
This paper describes the design methodology used
to create the ZFIN system, and the hybrid, web-accessible
interface developed to satisfy stringent usability
requirements.
- Eckehard Doerry, Sarah A. Douglas, Arthur E.
Kirkpatrick, Monte Westerfield. 1997. Participatory
Design for Widely-Distributed Scientific Communities.
Proceedings of the 3rd Conference on Human Factors
and the Web. This paper briefly examines the special
challenges of applying the user-centered design
methodology to widely-distributed scientific communities.
- Westerfield, M., E. Doerry, A.E. Kirkpatrick,
W. Driever and S.A. Douglas. 1997. An
on-line database for zebrafish development and genetics
research. Sem. Devel. Biol. 8:477-488. The Zebrafish
Database contents and use are described with examples
written for both biologists and computer scientists.
- Eckehard Doerry, Sarah A. Douglas, Ted Kirkpatrick,
Monte Westerfield. 1997. Task-centered
Navigation in Web-accessible Dataspaces. Position
Paper submitted to the WebNet97 Conference, Oct.
31-Nov.5, 1997, Toronto, Canada. This short paper
introduces the notion of using a representation
of known user tasks to provide navigational feedback
during multi-step transactions with a web-accessible
database.