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Zebrafish Information Network, the knowledgebase for Danio rerio research

Yvonne M Bradford, Ceri E Van Slyke, Leyla Ruzicka, Amy Singer, Anne Eagle, David Fashena, Douglas G Howe, Ken Frazer, Ryan Martin, Holly Paddock, Christian Pich, Sridhar Ramachandran (+1 others)
2022 Genetics  
Zebrafish Experimental Conditions Ontology (ZECO, Bradford et al. 2016), the Zebrafish Anatomical Ontology (ZFA, van Slyke et al. 2014), the Zebrafish Stage ontology (ZFS, van Slyke et al. 2014), GO cellular  ...  As previously noted, ZFIN data are also available via AllianceMine, API, and download files at the Alliance. al. 2013, Vasilevsky et al. 2013, Van Slyke et al. 2018).  ... 
doi:10.1093/genetics/iyac016 pmid:35166825 pmcid:PMC8982015 fatcat:v737talhbvbqdn4edyablydogi

The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio

Ceri E Van Slyke, Yvonne M Bradford, Monte Westerfield, Melissa A Haendel
2014 Journal of Biomedical Semantics  
The Zebrafish Anatomy Ontology (ZFA) is an OBO Foundry ontology that is used in conjunction with the Zebrafish Stage Ontology (ZFS) to describe the gross and cellular anatomy and development of the zebrafish, Danio rerio, from single cell zygote to adult. The zebrafish model organism database (ZFIN) uses the ZFA and ZFS to annotate phenotype and gene expression data from the primary literature and from contributed data sets. Results: The ZFA models anatomy and development with a subclass
more » ... hy, a partonomy, and a developmental hierarchy and with relationships to the ZFS that define the stages during which each anatomical entity exists. The ZFA and ZFS are developed utilizing OBO Foundry principles to ensure orthogonality, accessibility, and interoperability. The ZFA has 2860 classes representing a diversity of anatomical structures from different anatomical systems and from different stages of development. Conclusions: The ZFA describes zebrafish anatomy and development semantically for the purposes of annotating gene expression and anatomical phenotypes. The ontology and the data have been used by other resources to perform cross-species queries of gene expression and phenotype data, providing insights into genetic relationships, morphological evolution, and models of human disease.
doi:10.1186/2041-1480-5-12 pmid:24568621 pmcid:PMC3944782 fatcat:bmhhm3n4dzfuba3tkwnkfzoee4

Automated generation of gene summaries at the Alliance of Genome Resources

Ranjana Kishore, Valerio Arnaboldi, Ceri E Van Slyke, Juancarlos Chan, Robert S Nash, Jose M Urbano, Mary E Dolan, Stacia R Engel, Mary Shimoyama, Paul W Sternberg, the Alliance of Genome Resources
2020 Database: The Journal of Biological Databases and Curation  
We also thank Kimberly Van Auken, Peter D'Eustachio, Yvonne Bradford, Nomi Harris and Chris Mungall for discussions related to the project and for comments and suggestions on the manuscript.  ... 
doi:10.1093/database/baaa037 pmid:32559296 pmcid:PMC7304461 fatcat:sqmafymva5htzjv3sauiipkote

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  
Slyke et al., 2014) .  ...  The interface is a standard search and filter mechanism used in many e-commerce sites as well as at Ensembl and PubMed.  ... 
doi:10.1002/dvg.22868 pmid:26097180 pmcid:PMC4545674 fatcat:tba5jdejl5grxavmzhzgzjfcpa

A Unified Anatomy Ontology of the Vertebrate Skeletal System

Wasila M. Dahdul, James P. Balhoff, David C. Blackburn, Alexander D. Diehl, Melissa A. Haendel, Brian K. Hall, Hilmar Lapp, John G. Lundberg, Christopher J. Mungall, Martin Ringwald, Erik Segerdell, Ceri E. Van Slyke (+4 others)
2012 PLoS ONE  
The skeleton is of fundamental importance in research in comparative vertebrate morphology, paleontology, biomechanics, developmental biology, and systematics. Motivated by research questions that require computational access to and comparative reasoning across the diverse skeletal phenotypes of vertebrates, we developed a module of anatomical concepts for the skeletal system, the Vertebrate Skeletal Anatomy Ontology (VSAO), to accommodate and unify the existing skeletal terminologies for the
more » ... ecies-specific (mouse, the frog Xenopus, zebrafish) and multispecies (teleost, amphibian) vertebrate anatomy ontologies. Previous differences between these terminologies prevented even simple queries across databases pertaining to vertebrate morphology. This module of upper-level and specific skeletal terms currently includes 223 defined terms and 179 synonyms that integrate skeletal cells, tissues, biological processes, organs (skeletal elements such as bones and cartilages), and subdivisions of the skeletal system. The VSAO is designed to integrate with other ontologies, including the Common Anatomy Reference Ontology (CARO), Gene Ontology (GO), Uberon, and Cell Ontology (CL), and it is freely available to the community to be updated with additional terms required for research. Its structure accommodates anatomical variation among vertebrate species in development, structure, and composition. Annotation of diverse vertebrate phenotypes with this ontology will enable novel inquiries across the full spectrum of phenotypic diversity.
doi:10.1371/journal.pone.0051070 pmid:23251424 pmcid:PMC3519498 fatcat:bqn6ahk3v5dxdja63dsslhu3aq

The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability

Alexander D. Diehl, Terrence F. Meehan, Yvonne M. Bradford, Matthew H. Brush, Wasila M. Dahdul, David S. Dougall, Yongqun He, David Osumi-Sutherland, Alan Ruttenberg, Sirarat Sarntivijai, Ceri E. Van Slyke, Nicole A. Vasilevsky (+3 others)
2016 Journal of Biomedical Semantics  
The Cell Ontology (CL) is an OBO Foundry candidate ontology covering the domain of canonical, natural biological cell types. Since its inception in 2005, the CL has undergone multiple rounds of revision and expansion, most notably in its representation of hematopoietic cells. For in vivo cells, the CL focuses on vertebrates but provides general classes that can be used for other metazoans, which can be subtyped in species-specific ontologies. Construction and content: Recent work on the CL has
more » ... ocused on extending the representation of various cell types, and developing new modules in the CL itself, and in related ontologies in coordination with the CL. For example, the Kidney and Urinary Pathway Ontology was used as a template to populate the CL with additional cell types. In addition, subtypes of the class 'cell in vitro' have received improved definitions and labels to provide for modularity with the representation of cells in the Cell Line Ontology and Reagent Ontology. Recent changes in the ontology development methodology for CL include a switch from OBO to OWL for the primary encoding of the ontology, and an increasing reliance on logical definitions for improved reasoning. Utility and discussion: The CL is now mandated as a metadata standard for large functional genomics and transcriptomics projects, and is used extensively for annotation, querying, and analyses of cell type specific data in sequencing consortia such as FANTOM5 and ENCODE, as well as for the NIAID ImmPort database and the Cell Image Library. The CL is also a vital component used in the modular construction of other biomedical ontologies-for example, the Gene Ontology and the cross-species anatomy ontology, Uberon, use CL to support the consistent representation of cell types across different levels of anatomical granularity, such as tissues and organs. Conclusions: The ongoing improvements to the CL make it a valuable resource to both the OBO Foundry community and the wider scientific community, and we continue to experience increased interest in the CL both among developers and within the user community.
doi:10.1186/s13326-016-0088-7 pmid:27377652 pmcid:PMC4932724 fatcat:otjugknudng4vilqqufaxppst4

The Zebrafish Information Network: major gene page and home page updates

Douglas G Howe, Sridhar Ramachandran, Yvonne M Bradford, David Fashena, Sabrina Toro, Anne Eagle, Ken Frazer, Patrick Kalita, Prita Mani, Ryan Martin, Sierra Taylor Moxon, Holly Paddock (+7 others)
2020 Nucleic Acids Research  
The Zebrafish Information Network (ZFIN) (https://zfin.org/) is the database for the model organism, zebrafish (Danio rerio). ZFIN expertly curates, organizes, and provides a wide array of zebrafish genetic and genomic data, including genes, alleles, transgenic lines, gene expression, gene function, mutant phenotypes, orthology, human disease models, gene and mutant nomenclature, and reagents. New features at ZFIN include major updates to the home page and the gene page, the two most used pages
more » ... at ZFIN. Data including disease models, phenotypes, expression, mutants and gene function continue to be contributed to The Alliance of Genome Resources for integration with similar data from other model organisms.
doi:10.1093/nar/gkaa1010 pmid:33170210 pmcid:PMC7778988 fatcat:sofsxiaecncnnkvkeh3y5nwem4

ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics

Douglas G. Howe, Yvonne M. Bradford, Tom Conlin, Anne E. Eagle, David Fashena, Ken Frazer, Jonathan Knight, Prita Mani, Ryan Martin, Sierra A. Taylor Moxon, Holly Paddock, Christian Pich (+9 others)
2012 Nucleic Acids Research  
At ZFIN, phenotypes are represented using the EQ syntax to create phenotype statements, where E represents the entity (an anatomical structure or GOBP) and Q is the phenotypic quality from the Phenotypic  ... 
doi:10.1093/nar/gks938 pmid:23074187 pmcid:PMC3531097 fatcat:uzddasd6qrhjvmphh7z4qtp3ay

The Zebrafish Information Network: new support for non-coding genes, richer Gene Ontology annotations and the Alliance of Genome Resources

Leyla Ruzicka, Douglas G Howe, Sridhar Ramachandran, Sabrina Toro, Ceri E Van Slyke, Yvonne M Bradford, Anne Eagle, David Fashena, Ken Frazer, Patrick Kalita, Prita Mani, Ryan Martin (+7 others)
2018 Nucleic Acids Research  
The Zebrafish Information Network (ZFIN) (https://zfin.org/) is the database for the model organism, zebrafish (Danio rerio). ZFIN expertly curates, organizes and provides a wide array of zebrafish genetic and genomic data, including genes, alleles, transgenic lines, gene expression, gene function, mutant phenotypes, orthology, human disease models, nomenclature and reagents. New features at ZFIN include increased support for genomic regions and for non-coding genes, and support for more
more » ... ive Gene Ontology annotations. ZFIN has recently taken over maintenance of the zebrafish reference genome sequence as part of the Genome Reference Consortium. ZFIN is also a founding member of the Alliance of Genome Resources, a collaboration of six model organism databases (MODs) and the Gene Ontology Consortium (GO). The recently launched Alliance portal (https://alliancegenome.org) provides a unified, comparative view of MOD, GO, and human data, and facilitates foundational and translational biomedical research.
doi:10.1093/nar/gky1090 pmid:30407545 pmcid:PMC6323962 fatcat:dhrucy7vmve75jckjuofnine2e

OBO Foundry in 2021: Operationalizing Open Data Principles to Evaluate Ontologies [article]

Rebecca C Jackson, Nicolas Matentzoglu, James A Overton, Randi Vita, James P Balhoff, Pier Luigi Buttigieg, Seth Carbon, Melanie Courtot, Alexander D Diehl, Damion Dooley, William Duncan, Nomi L Harris (+13 others)
2021 bioRxiv   pre-print
We thank the members of the OBO community who have provided feedback on the dashboard, including Chris Grove, Ceri van Slyke, Sebastian Koehler, James Seager, Anne Thessen, Sue Bello, Midori Harris, Hilmar  ... 
doi:10.1101/2021.06.01.446587 fatcat:dygr55ijq5bhbc4uma4zkvjpwm

Effect upon Growth of the D Isomers in Synthetic Mixtures of the Essential Amino Acids

William A. Phillips, Clarence P. Berg
1954 Journal of Nutrition  
All of the amino acids were recrystallized to give correct amino nitrogen or total nitrogen values, as determined by the Van Slyke and Kjeldahl methods.  ...  VAN EtTren 1932 The availability of d-tryptophane and its acetyl derivative to the animal body. Ibid., 98: 565-575. West, H. D., anp H. E.  ... 
doi:10.1093/jn/53.4.481 pmid:13212429 fatcat:bg4ew2nff5bafh5omj7h5yst54

Index of authors' names

1916 Journal of the Chemical Society Abstracts  
Slyke, Lucius LincoZ?L van, aild Alfred W. Bosworth, chemical ch,~nges in the souring of milk. A., i, 354. Slyke, Lueizcs Lincoln can. See alqo Alfred V. Bosworth. Smid, (Hiss) E. I.  ...  Slyke, Uonald D. van, and Glem R Cullen, estimation of urea by the iirease method, A., ii, %03. Slyke, Donald D. Tan, Nariant Vinograd Villchur, awl J. B.  ...  Meek, the iratiu-e of tlic v i h r i o n s rausiiig the colonr of dyes, A . , ii, 2. Watson, Xd~j1'71 1Zu?  ... 
doi:10.1039/ca9161005657 fatcat:wf7pwvajgndillwyrc6jpvwala

THE USE OF INTARVIN IN DIABETES MELLITUS

D M Lyon, W Robson, A C White
1925 The BMJ (British Medical Journal) (Print)  
On March 12th on this diet it was found that the blood acetone (Van Slyke and Fitz) rose to 100 mg. per cent. two hours after breakfast, falling to 9 mg. per cent. two hours later, and remaining at this  ...  Sevriglhaus'' repolts that after comiiparing tIme effect of ingestioni of beef suet anid ai e(qual (quantity of glyceryl margarate in a ketonuria fo)llowing er hvdr1 ate-.sta 4rvtion-"Gly-cery 1 margarate  ... 
pmid:20771894 pmcid:PMC2196799 fatcat:cttvxv7iwbe7vid2zxlgvujimu

OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies

Rebecca Jackson, Nicolas Matentzoglu, James A Overton, Randi Vita, James P Balhoff, Pier Luigi Buttigieg, Seth Carbon, Melanie Courtot, Alexander D Diehl, Damion M Dooley, William D Duncan, Nomi L Harris (+13 others)
2021 Database: The Journal of Biological Databases and Curation  
Acknowledgements The authors thank the members of the OBO community who have provided feedback on the dashboard, including Chris Grove, Ceri van Slyke, Sebastian Koehler, James Seager, Anne Thessen, Sue  ... 
doi:10.1093/database/baab069 pmid:34697637 pmcid:PMC8546234 fatcat:x7bahrdhnjf3dkfnekjx45gty4

Page 1877 of Evangelist and Religious Review Vol. 46, Issue 42 [page]

1875 Evangelist and Religious Review  
E. Van Slyke and Stamford, Ct., Rocky Spring church, where this service greater number of ministers of whom as ties to estates over 200 years old. ^ was dissolved. books.  ...  The mission school is under the charge of , , , •E> - xi some of these men .are always hovenng. Rev. A. G.  ... 
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