Resource Informatics and Production Core Discovering the functions of the tens of thousands of genes in the human genome is a required step for understanding human biology and disease. Genetic model organisms, including zebrafish, play a critical role in this discovery process, because genetic analysis can connect gene sequence and function. Model organism databases, like ZFIN, provide tools required to make this connection. The zebrafish has emerged as a premier organism to study vertebrate biology. Powerful techniques allow rapid efficient generation and recovery of mutations affecting genes that orchestrate developmental patterning, organogenesis, physiology, and behavior. It is easy to study gene function by generating transgenic zebrafish, by knocking down gene function with morpholino antisense oligonucleotides, or by altering gene function by genome editing. The genome has been sequenced and about 50% of the protein coding genes have been mutated by targeted gene knockout technology. Large-scale projects are underway or planned that will produce functional data about almost all the genes and sequence-based functional elements in the genome. Multiple mutations and gene knockdowns can be combined in the same individual to study gene modifiers and other genetic interactions. The functions of most of these genes are conserved among vertebrate groups. Thus, analysis of zebrafish mutations provides insights into gene functions in other vertebrates, including humans. 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, developmental, and physiological 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 help serve the broad needs of the biomedical research community. This core will make ZFIN data widely accessible. We will continue to make the entire ZFIN database publically available, including bulk downloads, processing, and analysis. We will develop the infrastructure necessary to annotate the genome and make it available through Ensembl, UCSC, NCBI, ZFIN, and other browsers. We will develop and improve curator interfaces to improve the efficiency of curation, and we will migrate the ZFIN database server platform from Informix to PostgreSQL.
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| The Gene Ontology Consortium (2017) Expansion of the Gene Ontology knowledgebase and resources. Nucleic Acids Res 45:D331-D338 |
| Howe, Douglas G; Bradford, Yvonne M; Eagle, Anne et al. (2017) The Zebrafish Model Organism Database: new support for human disease models, mutation details, gene expression phenotypes and searching. Nucleic Acids Res 45:D758-D768 |
| Bradford, Yvonne M; Toro, Sabrina; Ramachandran, Sridhar et al. (2017) Zebrafish Models of Human Disease: Gaining Insight into Human Disease at ZFIN. ILAR J 58:4-16 |
| Huntley, Rachael P; Sitnikov, Dmitry; Orlic-Milacic, Marija et al. (2016) Guidelines for the functional annotation of microRNAs using the Gene Ontology. RNA 22:667-76 |
| Edmunds, Richard C; Su, Baofeng; Balhoff, James P et al. (2016) Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes. Mol Biol Evol 33:13-24 |
| Howe, D G; Bradford, Y M; Eagle, A et al. (2016) A scientist's guide for submitting data to ZFIN. Methods Cell Biol 135:451-81 |
| Diehl, Alexander D; Meehan, Terrence F; Bradford, Yvonne M et al. (2016) The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability. J Biomed Semantics 7:44 |
| Van Slyke, Ceri E; Bradford, Yvonne M; Westerfield, Monte et al. (2014) The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio. J Biomed Semantics 5:12 |
| Haendel, Melissa A; Balhoff, James P; Bastian, Frederic B et al. (2014) Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon. J Biomed Semantics 5:21 |
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