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The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes
2007
Nucleic Acids Research
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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
2003
Nucleic Acids Research
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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
2006
Nucleic Acids Research
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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
2015
Genesis
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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
2017
Genetics
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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
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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
2007
Journal of Experimental Zoology Part B: Molecular and Developmental Evolution
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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
2014
F1000Research
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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
2014
F1000Research
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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
2015
Nucleic Acids Research
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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
2007
Trends in Ecology & Evolution
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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]
2021
bioRxiv
pre-print
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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
2013
Database: The Journal of Biological Databases and Curation
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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
2009
PLoS Biology
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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
2017
Seminars in Cell and Developmental Biology
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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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