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The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes

J. Sprague, L. Bayraktaroglu, Y. Bradford, T. Conlin, N. Dunn, D. Fashena, K. Frazer, M. Haendel, D. G. Howe, J. Knight, P. Mani, S. A.T. Moxon (+10 others)
2007 Nucleic Acids Research  
The Zebrafish Information Network (ZFIN, http:// zfin.org), the model organism database for zebrafish, provides the central location for curated zebrafish genetic, genomic and developmental data.  ...  Recent enhancements to ZFIN include (i) a new home page and navigation bar, (ii) expanded support for genotypes and phenotypes, (iii) comprehensive phenotype annotations based on anatomical, phenotypic  ...  ACKNOWLEDGEMENTS Funds for the development of the Zebrafish Information Network are provided by the NIH HG002659.  ... 
doi:10.1093/nar/gkm956 pmid:17991680 pmcid:PMC2238839 fatcat:3jookkeqbfbifhku6ymfqsns7q

The Zebrafish Information Network (ZFIN): the zebrafish model organism database

J. Sprague
2003 Nucleic Acids Research  
The Zebrafish Information Network (ZFIN) is a web based community resource that serves as a centralized location for the curation and integration of zebrafish genetic, genomic and developmental data.  ...  ACKNOWLEDGEMENT Funds for the development of the Zebrafish Information Network are provided by the NIH (RR/HD 12546).  ...  The long term plan is for ZFIN to serve as the repository for this information, integrating annotated sequence with ZFIN genotype, phenotype and gene expression data.  ... 
doi:10.1093/nar/gkg027 pmid:12519991 pmcid:PMC165474 fatcat:5yyclbuwuzc5vhny2ueudbgrge

The Zebrafish Information Network: the zebrafish model organism database

J. Sprague
2006 Nucleic Acids Research  
10 The Zebrafish Information Network (ZFIN; http://zfin. org) is a web based community resource that implements the curation of zebrafish genetic, genomic and developmental data.  ...  , (iii) expanded use of ontologies to support curation and query forms, (iv) curation of morpholino data from the literature, and (v) increased versatility of gene pages, with new data 25 types, links  ...  ACKNOWLEDGEMENTS 5 Funds for the development of the Zebrafish Information Network are provided by the NIH HG002659.  ... 
doi:10.1093/nar/gkj086 pmid:16381936 pmcid:PMC1347449 fatcat:hn2czv6dkbg2rjpedqetwwym5i

ZFIN, The zebrafish model organism database: Updates and new directions

Leyla Ruzicka, Yvonne M. Bradford, Ken Frazer, Douglas G. Howe, Holly Paddock, Sridhar Ramachandran, Amy Singer, Sabrina Toro, Ceri E. Van Slyke, Anne E. Eagle, David Fashena, Patrick Kalita (+8 others)
2015 Genesis  
The Zebrafish Model Organism Database (ZFIN; http://zfin.org) is the central resource for genetic and genomic data from zebrafish (Danio rerio) research.  ...  The use of zebrafish as a model for human disease is increasing.  ...  Acknowledgments Grant Support: This work was supported by the National Human Genome Research Institute (HG002659, and HG004834) of the National Institutes of Health.  ... 
doi:10.1002/dvg.22868 pmid:26097180 pmcid:PMC4545674 fatcat:tba5jdejl5grxavmzhzgzjfcpa

Model Organisms Facilitate Rare Disease Diagnosis and Therapeutic Research

Michael F. Wangler, Shinya Yamamoto, Hsiao-Tuan Chao, Jennifer E. Posey, Monte Westerfield, John Postlethwait, Philip Hieter, Kym M. Boycott, Philippe M. Campeau, Hugo J. Bellen
2017 Genetics  
Material, File S1) and UDN International (UDNI), the Centers for Mendelian Genomics (CMG), and the Canadian Rare Diseases Models and Mechanisms Network (RDMM).  ...  Diagnostic challenges posed by undiagnosed diseases have solutions in model organism research, which provides a wealth of detailed biological information.  ...  Maintaining and expanding the resources of model organism communities will provide invaluable information to expand our ability to diagnose and dissect the molecular mechanisms underlying human diseases  ... 
doi:10.1534/genetics.117.203067 pmid:28874452 pmcid:PMC5586389 fatcat:bhaf43bq45dcnnjuoklczpm5ui

The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species

2019 Nucleic Acids Research  
The Monarch Initiative (https://monarchinitiative.org) integrates information on genes, variants, genotypes, phenotypes and diseases in a variety of species, and allows powerful ontology-based search.  ...  Our algorithms and tools are widely used to identify animal models of human disease through phenotypic similarity, for differential diagnostics and to facilitate translational research.  ...  ACKNOWLEDGEMENTS We would like to thank the many people who have contributed to the improvements and updates we have reported here, including (but not limited to) Donna Maglott, Anne Pariser and Janine  ... 
doi:10.1093/nar/gkz997 pmid:31701156 pmcid:PMC7056945 fatcat:tramusfgz5eufn2aguuzzasafi

Connecting evolutionary morphology to genomics using ontologies: a case study from Cypriniformes including zebrafish

Paula M. Mabee, Gloria Arratia, Miles Coburn, Melissa Haendel, Eric J. Hilton, John G. Lundberg, Richard L. Mayden, Nelson Rios, Monte Westerfield
2007 Journal of Experimental Zoology Part B: Molecular and Developmental Evolution  
qualities that are applicable to any organism http://www.bioontology.org/wiki/ index.php/PATO: Main_Page ZFIN-Zebrafish Information Network, the model organism database for zebrafish http://www.zfin.org  ...  We will utilize both existing and new ontologies to connect the evolutionary anatomy and image database that is being developed in the Cypriniformes Tree of Life project to the Zebrafish Information Network  ...  ACKNOWLEDGMENTS We thank the NSF National Evolutionary Synthesis Center (EF-0423641), NSF Cypriniformes Tree of Life (DEB-0431290), NIH HG002659 and HG004028 for support.  ... 
doi:10.1002/jez.b.21181 pmid:17599725 fatcat:g3zxqegl2jherodstnvyfo2kwm

Yeast Augmented Network Analysis (YANA): a new systems approach to identify therapeutic targets for human genetic diseases

David J. Wiley, Ilona Juan, Hao Le, Xiaodong Cai, Lisa Baumbach, Christine Beattie, Gennaro D'Urso
2014 F1000Research  
Third, from UBA1 these networks we identified potential therapeutic targets for SMA. Finally, we validate one of these targets in a vertebrate (zebrafish) SMA model.  ...  This study demonstrates the power of combining synthetic and chemical genetics with a simple model system to identify human disease gene networks that can be exploited for treating human diseases.  ...  Goldschmidt for their encouragement and discussions during the early phase of these studies.  ... 
doi:10.12688/f1000research.4484 fatcat:wuvhj2n2qbcangvwqy5nn72o7q

Yeast Augmented Network Analysis (YANA): a new systems approach to identify therapeutic targets for human genetic diseases

David J. Wiley, Ilona Juan, Hao Le, Xiaodong Cai, Lisa Baumbach, Christine Beattie, Gennaro D'Urso
2014 F1000Research  
Third, from these networks we identified potential therapeutic targets for SMA. Finally, we validate one of these targets in a vertebrate (zebrafish) SMA model.  ...  This study demonstrates the power of combining synthetic and chemical genetics with a simple model system to identify human disease gene networks that can be exploited for treating human diseases.  ...  Goldschmidt for their encouragement and discussions during the early phase of these studies.  ... 
doi:10.12688/f1000research.4188.1 pmid:25075304 pmcid:PMC4097366 fatcat:acyfywp3t5g57pk2bm3zjeenn4

MouseNet v2: a database of gene networks for studying the laboratory mouse and eight other model vertebrates

Eiru Kim, Sohyun Hwang, Hyojin Kim, Hongseok Shim, Byunghee Kang, Sunmo Yang, Jae Ho Shim, Seung Yeon Shin, Edward M. Marcotte, Insuk Lee
2015 Nucleic Acids Research  
Furthermore, MouseNet v2 database provides functional networks for eight other vertebrate models used in various research fields.  ...  The network database has been substantially improved by large expansion of genomics data.  ...  The MGI database (5) provides mouse orthology information for these vertebrate models, so we expanded the MouseNet v2 server to allow network searches for genes of these model vertebrates.  ... 
doi:10.1093/nar/gkv1155 pmid:26527726 pmcid:PMC4702832 fatcat:pw434vapczcmtpxst4jas6pfgm

Phenotype ontologies: the bridge between genomics and evolution

P MABEE, M ASHBURNER, Q CRONK, G GKOUTOS, M HAENDEL, E SEGERDELL, C MUNGALL, M WESTERFIELD
2007 Trends in Ecology & Evolution  
By contrast, model organism studies have been enhanced by ontologies shared among genomic databases.  ...  Here, we suggest that evolutionary and genomics databases can be developed to exchange and use information through shared phenotype and anatomy ontologies.  ...  G.V.G. is supported by the National Center for Biomedical Ontology (NIH: 1-U54-HG004028-01). We thank Adam Amsterdam and Nancy Hopkins for use of the image in Figure 2 .  ... 
doi:10.1016/j.tree.2007.03.013 pmid:17416439 fatcat:lub7w3xaxbghhcf7ygb7c2o36a

Gene network module changes associated with the vertebrate fin to limb transition [article]

Pasan C Fernando, Paula M Mabee, Erliang Zeng
2021 bioRxiv   pre-print
This paper presents the results of our investigations and demonstrates a general network-based computational workflow to study evolutionary phenotypic transitions involving diverse model organisms and  ...  To expand the number of analyzed genes and hence, biological knowledge, we computationally isolated and compared the gene modules for paired fins (pectoral fin, pelvic fin) of fishes (zebrafish) to those  ...  These methods start 93 from a set of known genes for a given phenotype and expand the module based on the network 94 structure.  ... 
doi:10.1101/2021.01.28.428646 fatcat:wvzerv43cjdjdnfkvnfbvpv7jy

PhenoDigm: analyzing curated annotations to associate animal models with human diseases

D. Smedley, A. Oellrich, S. Kohler, B. Ruef, M. Westerfield, P. Robinson, S. Lewis, C. Mungall
2013 Database: The Journal of Biological Databases and Curation  
C.M. and S.L. provided the OWLSim source code, guidance and support and how to apply OWLSim to the input data.  ...  S.K. and P.R. generated the pre-composed version of zebrafish annotations (ZP), that was then curated and corrected by B.R. and M.W.  ...  Here, we present Phenotype comparisons for DIsease Genes and Models (PhenoDigm): a database and application that enables the connection of model organisms to human diseases based on phenotype information  ... 
doi:10.1093/database/bat025 pmid:23660285 pmcid:PMC3649640 fatcat:5c5jjafnbzbrrdsodzw4xe2ghq

Linking Human Diseases to Animal Models Using Ontology-Based Phenotype Annotation

Nicole L. Washington, Melissa A. Haendel, Christopher J. Mungall, Michael Ashburner, Monte Westerfield, Suzanna E. Lewis, Kenneth H. Buetow
2009 PLoS Biology  
These human annotations were loaded into our Ontology-Based Database (OBD) along with other ontology-based phenotype descriptions of mutants from various model organism databases.  ...  The considerable variation in these free-text descriptions has posed a hindrance to the important task of identifying candidate genes and models for human diseases and indicates the need for a computationally  ...  Acknowledgments We thank Yvonne Bradford, Amy Singer, and Erik Segerdell for their annotation efforts; Robert Bruggner for contributions to the OBD system; and Drs.  ... 
doi:10.1371/journal.pbio.1000247 pmid:19956802 pmcid:PMC2774506 fatcat:afqpxkwuwnbrze4bawkwwln2ea

Building dialogues between clinical and biomedical research through cross-species collaborations

Hsiao-Tuan Chao, Lucy Liu, Hugo J. Bellen
2017 Seminars in Cell and Developmental Biology  
organism approaches to uncover the biological underpinnings of health and disease.  ...  The goal of this review is to provide examples of diverse strategies to enhance communication and collaboration across diverse disciplines.  ...  We are grateful for the support from the Robert A. and Renee E. Belfer Family Foundation, the Huffington Foundation, and Target  ... 
doi:10.1016/j.semcdb.2017.05.022 pmid:28579453 pmcid:PMC5623622 fatcat:sf3leqss5rezfmkg4jiezpogwy
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