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Biological Database of Images and Genomes: tools for community annotations linking image and genomic information

Andrew T Oberlin, Dominika A Jurkovic, Mitchell F Balish, Iddo Friedberg
2013 Database: The Journal of Biological Databases and Curation  
., Balish,M.F. and Friedberg,I. Biological database of Images and Genomes: tools for community annotations linking image and genomic information.  ...  By using BioDIG to create websites, researchers and curators can rapidly annotate a large number of images with genomic information.  ...  Microscopy was performed at the Miami University Center for Advanced Microscopy Imaging. We Conflict of interest. None declared.  ... 
doi:10.1093/database/bat016 pmid:23550062 pmcid:PMC3708683 fatcat:r72yswwixvfapcqnlgfznunyw4

Biological Database of Images and Genomes: tools for community annotations linking image and genomic information [article]

Andrew T. Oberlin, Dominika A. Jurkovic, Mitchell F. Balish, Iddo Friedberg
2012 arXiv   pre-print
By using BioDIG to create websites, researchers and curators can rapidly annotate large number of images with genomic information.  ...  While there are many types of software that enable the manipulation and analysis of image data and genomic data as separate entities, there is no framework established for linking the two.  ...  Here we present the Biological Database of Images and Genomes or BioDIG. BioDIG is a set of tools to construct databases with genomic and image data and place them in semantic association.  ... 
arXiv:1212.0447v1 fatcat:vtxuked4w5cvpa4aeo4hfdgere

Mining biomedical images towards valuable information retrieval in biomedical and life sciences

Zeeshan Ahmed, Saman Zeeshan, Thomas Dandekar
2016 Database: The Journal of Biological Databases and Curation  
and analysis of text and content in biomedical images to take advantage in implementing effective information retrieval systems.  ...  In last decades, there has been an enormous increase in the amount of heterogeneous biomedical image production and publication, which results in a need for bioimaging platforms for feature extraction  ...  We would like to thank all supporting institutes during this research, especially to the University of Wuerzburg Germany and the Jackson Laboratory for Genomic Medicine USA.  ... 
doi:10.1093/database/baw118 pmid:27538578 pmcid:PMC4990152 fatcat:dlyhrh5nxjhutlvvw2qkgx3wei

MaizeGDB 2018: the maize multi-genome genetics and genomics database

John L Portwood, Margaret R Woodhouse, Ethalinda K Cannon, Jack M Gardiner, Lisa C Harper, Mary L Schaeffer, Jesse R Walsh, Taner Z Sen, Kyoung Tak Cho, David A Schott, Bremen L Braun, Miranda Dietze (+9 others)
2018 Nucleic Acids Research  
visualize pedigree data (Pedigree Viewer), link genes with phenotype images (MaizeDIG), and enable flexible user-specified queries to the MaizeGDB database (MaizeMine).  ...  Since its 2015 update, MaizeGDB, the Maize Genetics and Genomics database, has expanded to support the sequenced genomes of many maize inbred lines in addition to the B73 reference genome assembly.  ...  We would like to give a special thank you to Ed Coe as not only the founder of the original Maize Genetics Database and continued contributor to the database, but also for his contribution to the generation  ... 
doi:10.1093/nar/gky1046 pmid:30407532 fatcat:4kigm7hldzfxpmy6zpwwxsqki4

Kiwifruit Genome Database (KGD): a comprehensive resource for kiwifruit genomics

Junyang Yue, Jiacheng Liu, Wei Tang, Ya Qing Wu, Xiaofeng Tang, Wei Li, Ying Yang, Lihuan Wang, Shengxiong Huang, Congbing Fang, Kun Zhao, Zhangjun Fei (+2 others)
2020 Horticulture Research  
Since the release of the first kiwifruit reference genome sequence in 2013, large volumes of genome and transcriptome data have been rapidly accumulated for a handful of kiwifruit species.  ...  The database currently contains all publicly available genome and gene sequences, gene annotations, biochemical pathways, transcriptome profiles derived from public RNA-Seq datasets, and comparative genomic  ...  Acknowledgements This study was supported by grants from the National Natural Science Conflict of interest The authors declare that they have no conflict of interest.  ... 
doi:10.1038/s41438-020-0338-9 pmid:32821400 pmcid:PMC7395147 fatcat:hrkefpgi2vdgdpv233fuqse75q

MaizeDIG: Maize Database of Images and Genomes

Kyoung Tak Cho, John L. Portwood, Jack M. Gardiner, Lisa C. Harper, Carolyn J. Lawrence-Dill, Iddo Friedberg, Carson M. Andorf
2019 Frontiers in Plant Science  
To integrate mutant phenotype images with genomics information, we implemented and enhanced the web-based software package BioDIG (Biological Database of Images and Genomes).  ...  This is accomplished through an updated interface allowing users to create image-to-gene links and is accessible via the image search tool.  ...  Gerald Neuffer for providing his collection of mutant phenotype images to MaizeGDB, and Andrew Oberlin and personnel working in the Friedberg laboratory for support for BioDIG installation.  ... 
doi:10.3389/fpls.2019.01050 pmid:31555312 pmcid:PMC6724615 fatcat:c3bno4adzvahjnxukki7kuiq4y

Tools and strategies for physiological genomics: the Rat Genome Database

Simon N. Twigger, Dean Pasko, Jeff Nie, Mary Shimoyama, Susan Bromberg, Dan Campbell, Jiali Chen, Norberto dela Cruz, Chunyu Fan, Cindy Foote, Glenn Harris, Brian Hickmann (+20 others)
2005 Physiological Genomics  
We present an overview of the database with a focus on these unique computational tools and describe strategies for the use of these resources in the area of physiological genomics.  ...  The Rat Genome Database (RGD; http://rgd. has developed computational tools and strategies specifically supporting the goal of linking genes to their functional roles in rat and, using comparative  ...  ACKNOWLEDGMENTS We thank Carol Moreno-Quinn for critical review of this manuscript and Brian Halligan for invaluable help with Acrobat.  ... 
doi:10.1152/physiolgenomics.00040.2005 pmid:16106031 pmcid:PMC4505745 fatcat:a5aranpv5feflcbwjqeddqxg4m

Genome Informatics

Raimond L. Winslow, Mark S. Boguski
2003 Circulation Research  
In each instance, we provide links to relevant sources of information on the World Wide Web and critical appraisals of the promises and the challenges of an expanding and diverse information landscape.  ...  In particular, we review the status of (1) whole genome sequencing efforts in human, mouse, rat, zebrafish, and dog; (2) the development of data mining and analysis tools; (3) the launching of the National  ...  Acknowledgments This work is supported by grants from the NIH (RO1 HL-61711, RO1 HL-60133, RO1 HL-72488, P50 HL-52307, N01 HV-28180), The Falk Medical Trust, and The Whitaker Foundation.  ... 
doi:10.1161/01.res.0000072475.04373.07 pmid:12750305 pmcid:PMC1237016 fatcat:p7ktapnt3fgkxnjj4k6tb3s36m

GOLD.db: genomics of lipid-associated disorders database

Hubert Hackl, Michael Maurer, Bernhard Mlecnik, Jürgen Hartler, Gernot Stocker, Diego Miranda-Saavedra, Zlatko Trajanoski
2004 BMC Genomics  
Analytic and data mining tools, reagents, protocols, references, and links to relevant genomic resources were included in the database.  ...  The main focus was to provide biological pathways with image maps and visual pathway information for lipid metabolism and obesity-related research.  ...  Acknowledgements This work was supported by the Austrian Science Fund, Project SFB Biomembranes F718, the GEN-AU projects Bioinformatics Integration Network (BIN) and Genomics of Lipid-Associated Disorders  ... 
doi:10.1186/1471-2164-5-93 pmid:15588328 pmcid:PMC544894 fatcat:d2o6c7vbpvdh5o6zbwihbacu5i

Mouse genome database 2016

Carol J. Bult, Janan T. Eppig, Judith A. Blake, James A. Kadin, Joel E. Richardson
2015 Nucleic Acids Research  
Recent enhancements to MGD include new graphical summaries of biological annotations for mouse genes, support for mobile access to the database, tools to support the annotation and analysis of sets of  ...  The Mouse Genome Database (MGD; http://www. is the primary community model organism database for the laboratory mouse and serves as the source for key biological reference data related  ...  The Mouse Genome Database (MGD) is the primary community resource for integrated genetic, genomic, functional and phenotypic information supporting the link between mouse models and human phenotypes and  ... 
doi:10.1093/nar/gkv1211 pmid:26578600 pmcid:PMC4702860 fatcat:ufv3jxfe55fdljxozjt6gzuayi

Xenbase: a Xenopus biology and genomics resource

J. B. Bowes, K. A. Snyder, E. Segerdell, R. Gibb, C. Jarabek, E. Noumen, N. Pollet, P. D. Vize
2007 Nucleic Acids Research  
Xenbase ( is a model organism database integrating a diverse array of biological and genomic data on the frogs, Xenopus laevis and Xenopus (Silurana) tropicalis.  ...  Data is collected from other databases, high-throughput screens and the scientific literature and integrated into a number of database modules covering subjects such as community, literature, gene and  ...  BLAST support is provided by the Center for Visual Genomics at the University of Calgary, Paul Gordon and Christoph Sensen.  ... 
doi:10.1093/nar/gkm826 pmid:17984085 pmcid:PMC2238855 fatcat:nwko67dfkneg5ai6flzyu7rq6q

Gramene, a Tool for Grass Genomics

D. H. Ware
2002 Plant Physiology  
Gramene ( is a comparative genome mapping database for grasses and a community resource for rice (Oryza sativa).  ...  Gramene curators read and extract detailed information from published sources, summarize that information in a structured format, and establish links to related objects both inside and outside the database  ...  with colleagues in the greater biological community.  ... 
doi:10.1104/pp.015248 pmid:12481044 fatcat:gzfiqjhh5jforkuockx23wrdfy

The Functional Magnetic Resonance Imaging Data Center (fMRIDC): the challenges and rewards of large-scale databasing of neuroimaging studies

J. D. Van Horn, J. S. Grethe, P. Kostelec, J. B. Woodward, J. A. Aslam, D. Rus, D. Rockmore, M. S. Gazzaniga
2001 Philosophical Transactions of the Royal Society of London. Biological Sciences  
We discuss how a publicly accessible database enables other ¢elds to develop relevant tools that can aid in the growth of understanding of cognitive processes.  ...  Information retrieval and meta-analytic techniques can be used to search, sort and categorize study information with a view towards subjecting study data to secondary'meta-' and'mega-analyses '.  ...  and genomic informatics.  ... 
doi:10.1098/rstb.2001.0916 pmid:11545705 pmcid:PMC1088517 fatcat:eegvyrf3i5aunja2gwu4uuaesm

WormBase 2012: more genomes, more data, new website

K. Yook, T. W. Harris, T. Bieri, A. Cabunoc, J. Chan, W. J. Chen, P. Davis, N. de la Cruz, A. Duong, R. Fang, U. Ganesan, C. Grove (+27 others)
2011 Nucleic Acids Research  
We report on the growth of our database and on our work in keeping pace with the growing demand for data, efforts to anticipate the requirements of users and new collaborations with the larger science  ...  To facilitate discovery, we have added new views of the data, integrated large-scale datasets and expanded descriptions of models for human disease.  ...  INCREASING THE EFFICIENCY OF ANNOTATION AND CURATION The need for efficient curation necessitates the development of customized curation tools.  ... 
doi:10.1093/nar/gkr954 pmid:22067452 pmcid:PMC3245152 fatcat:4jkq3undtzc6lporuvo3nteium

Bovine Genome Database: integrated tools for genome annotation and discovery

Christopher P. Childers, Justin T. Reese, Jaideep P. Sundaram, Donald C. Vile, C. Michael Dickens, Kevin L. Childs, Hanni Salih, Anna K. Bennett, Darren E. Hagen, David L. Adelson, Christine G. Elsik
2010 Nucleic Acids Research  
The initial goal of the Bovine Genome Database (BGD) project was to support the Bovine Genome Sequencing and Analysis Consortium by providing web-based tools for annotation of the bovine genome, and a  ...  There is also a tool for looking up protein homolog annotations, multiple flash tutorials that illustrate how to use Apollo to annotate genes and links to external databases and tools.  ...  Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkq1235 pmid:21123190 pmcid:PMC3013744 fatcat:a6soovwdmfcctcenz7uo5syfoy
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