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modMine: flexible access to modENCODE data

S. Contrino, R. N. Smith, D. Butano, A. Carr, F. Hu, R. Lyne, K. Rutherford, A. Kalderimis, J. Sullivan, S. Carbon, E. T. Kephart, P. Lloyd (+8 others)
2011 Nucleic Acids Research  
Interfaces are provided to allow both biologists and bioinformaticians to exploit these rich modENCODE data sets now available via modMine.  ...  The modMine database (http:// intermine.modencode.org) described here has been built by the modENCODE Data Coordination Center to allow the broader research community to (i) search for and download data  ...  CONCLUSION AND PLANS We have integrated data sets from the modENCODE project and relevant non-modENCODE data sets to make modMine a database that enables flexible interrogation of these combined resources  ... 
doi:10.1093/nar/gkr921 pmid:22080565 pmcid:PMC3245176 fatcat:nqghtnlqa5adxeeorq4vanlaum

Cloud-based uniform ChIP-Seq processing tools for modENCODE and ENCODE

Quang M Trinh, Fei-Yang Jen, Ziru Zhou, Kar Chu, Marc D Perry, Ellen T Kephart, Sergio Contrino, Peter Ruzanov, Lincoln D Stein
2013 BMC Genomics  
While the basic quality control, pre-processing, and analysis of the data has already been performed by members of the modENCODE consortium, many researchers will wish to reinterpret the data set using  ...  modifications and enhancements of the original protocols, or combine modENCODE data with other data sets.  ...  Traditional FTP access to the modENCODE data set is available from ftp://data.modencode.org.  ... 
doi:10.1186/1471-2164-14-494 pmid:23875683 pmcid:PMC3734164 fatcat:x5a4eoozb5eqdczxq7cy6ycgiq

The modENCODE Data Coordination Center: lessons in harvesting comprehensive experimental details

Nicole L. Washington, E. O. Stinson, Marc D. Perry, Peter Ruzanov, Sergio Contrino, Richard Smith, Zheng Zha, Rachel Lyne, Adrian Carr, Paul Lloyd, Ellen Kephart, Sheldon J. McKay (+3 others)
2011 Database: The Journal of Biological Databases and Curation  
M.D.P., Z.Z. and P.L. curated data. P.R. curated data and implemented GBrowse software. S.C. and R.S. implemented the modMine query interface and contributed to the design of the pipeline.  ...  It was chosen for the wide range of available tools, for its compatibility with the model organism databases (FB uses Chado, WB is considering migrating to it), and for the modENCODE DCC staff's familiarity  ...  an accession number to the DCC.  ... 
doi:10.1093/database/bar023 pmid:21856757 pmcid:PMC3170170 fatcat:5bbntrqslje2vhzxwx7vaegare

InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data

Richard N. Smith, Jelena Aleksic, Daniela Butano, Adrian Carr, Sergio Contrino, Fengyuan Hu, Mike Lyne, Rachel Lyne, Alex Kalderimis, Kim Rutherford, Radek Stepan, Julie Sullivan (+3 others)
2012 Bioinformatics  
The analysis tools include a flexible query builder, genomic region search and a library of 'widgets' performing various statistical analyses.  ...  Using InterMine, large biological databases can be created from a range of heterogeneous data sources, and the extensible data model allows for easy integration of new data types.  ...  ACKNOWLEDGEMENTS The authors would like to thank our users and collaborators for their continuing interest and support.  ... 
doi:10.1093/bioinformatics/bts577 pmid:23023984 pmcid:PMC3516146 fatcat:tczriadj3ze33f4zxm7gpw7iiu

toxoMine: an integrated omics data warehouse forToxoplasma gondiisystems biology research

David B. Rhee, Matthew McKnight Croken, Kevin R. Shieh, Julie Sullivan, Gos Micklem, Kami Kim, Aaron Golden
2015 Database: The Journal of Biological Databases and Curation  
As a data warehouse, toxoMine allows integration of high-throughput data sets with public T. gondii data. toxoMine is also able to execute complex queries involving multiple data sets with straightforward  ...  The interoperability feature also allows users to query and examine data available in other InterMine systems, which would effectively augment the search scope beyond what is available to toxoMine. toxoMine  ...  Toxoplasma gondii genomic sequence data and annotations were accessed via http://toxodb.org.  ... 
doi:10.1093/database/bav066 pmid:26130662 pmcid:PMC4485433 fatcat:lmhs4bis7zhzvhr6py6kb4y6hi

Considerations for creating and annotating the budding yeast Genome Map at SGD: a progress report

E. T. Chan, J. M. Cherry
2012 Database: The Journal of Biological Databases and Curation  
Acknowledgements We thank Edith Wong and Benjamin Hitz for their assistance in track setup and GBrowse configuration; Gail Binkley and Stuart Miyasato for adding the Genome Map data files to the downloads  ...  liftOver tool; Shuai Weng and Kalpana Karra for helpful discussions and the SGD biocurators for their work in classifying the literature and their assistance in defining the workflow for the Genome Map data  ...  Similarly, modMine, the metadata warehousing solution for the modENCODE project, is also built upon InterMine. modMine provides the interface for accessing modENCODE data files and querying metadata, which  ... 
doi:10.1093/database/bar057 pmid:22434826 pmcid:PMC3308148 fatcat:wwzz7etezvho3hd4fpbe4b44ia

Resources for Functional Genomics Studies in Drosophila melanogaster

Stephanie E. Mohr, Yanhui Hu, Kevin Kim, Benjamin E. Housden, Norbert Perrimon
2014 Genetics  
Here, we introduce key resources useful to plan large-scale functional genomics studies in Drosophila and to analyze, integrate, and mine the results of those studies in ways that facilitate identification  ...  Many resources, including online databases and software tools, are now available to support design or identification of relevant fly stocks and reagents or analysis and mining of existing functional genomic  ...  Acknowledgments We extend our thanks to Kathy Matthews and Annette Parks at the Bloomington Drosophila Stock Center and to Bill Gelbart, Susan St.  ... 
doi:10.1534/genetics.113.154344 pmid:24653003 pmcid:PMC4012471 fatcat:7n7iwcdva5bbxe2ewwdv3ny4d4

CBS: an open platform that integrates predictive methods and epigenetics information to characterize conserved regulatory features in multiple Drosophila genomes

Enrique Blanco, Montserrat Corominas
2012 BMC Genomics  
The rapid access to this novel body of knowledge through a user-friendly web interface enables non-expert users to identify the binding sequences available for any particular gene, transcription factor  ...  Conclusions: The CBS platform is a powerful resource that provides tools for data mining individual sequences and groups of co-expressed genes with epigenomics information to conduct regulatory screenings  ...  Acknowledgements We sincerely thank all the researchers involved in multiple international consortiums of genome sequencing, annotation, and visualization for granting open access of such resources to  ... 
doi:10.1186/1471-2164-13-688 pmid:23228284 pmcid:PMC3564944 fatcat:yukwy5bk3jhatmihapdcxtwme4

BioJS InterMineTable Component: A BioJS component for displaying data from InterMine compatible webservice endpoints

Alexis Kalderimis, Radek Stepan, Julie Sullivan, Rachel Lyne, Michael Lyne, Gos Micklem
2014 F1000Research  
Contrino S, Smith RN, Butano D, et al.: modMine: flexible access to modENCODE data. Nucleic Acids Res. 2012; 40(Database issue): D1082-1088. PubMed Abstract | Publisher Full Text | Free Full Text 4.  ...  It enables users to embed powerful table-based query facilities in their websites with access to genomic data-warehouses such as , which allow users to perform http://www.flymine.org flexible queries over  ...  In this way, the interoperability of these components makes them of increasing utility to developers, as more of them are published and integrated into third party applications.  ... 
doi:10.12688/f1000research.3-46.v1 fatcat:e7vyjr2ghzaeri73hgi5476mka

BioJS InterMine List Analysis: A BioJS component for displaying graphical or statistical analysis of collections of items from InterMine endpoints

Alexis Kalderimis, Radek Stepan, Julie Sullivan, Rachel Lyne, Michael Lyne, Gos Micklem
2014 F1000Research  
Contrino S, Smith RN, Butano D, et al.: modMine: flexible access to modENCODE data. Nucleic Acids Res. 2012; 40(Database issue): D1082-D1088. PubMed Abstract | Publisher Full Text | Free Full Text 4.  ...  It enables users to embed powerful table-based query facilities in their websites with access to genomic data-warehouses such as , which allow users to perform http://www.flymine.org flexible queries over  ...  By providing bioinformatics web-developers, and their users, with access to a broad range of data sources meeting the needs of many diverse research communities, we expect to help reduce the development  ... 
doi:10.12688/f1000research.3-45.v1 fatcat:wyhxnoegtjaidni2cyj57dcvmm

DANIO-CODE: Toward an Encyclopedia of DNA Elements in Zebrafish

Haihan Tan, Daria Onichtchouk, Cecilia Winata
2016 Zebrafish  
In this study, we provide the latest updates on the current progress of the consortium's efforts, opening up a broad invitation to researchers to join in and contribute to DANIO-CODE.  ...  The meeting brought together zebrafish researchers, bioinformaticians, as well as members of established consortia, to exchange scientific findings and experience, as well as to discuss the initial steps  ...  The organizers would also like to thank Jana Maier for help with organization of the workshop. C.W. is supported by the EU FP7 Grant FishMed GA No. 316125 and D.O. is supported by A7-DFG-EXC294.  ... 
doi:10.1089/zeb.2015.1179 pmid:26671609 pmcid:PMC4742988 fatcat:2yr6iyy5lnag3indn3u2yoi5ne

InterMine: extensive web services for modern biology

Alex Kalderimis, Rachel Lyne, Daniela Butano, Sergio Contrino, Mike Lyne, Joshua Heimbach, Fengyuan Hu, Richard Smith, Radek Štěpán, Julie Sullivan, Gos Micklem
2014 Nucleic Acids Research  
in many other applications: to find and filter data; export it in a flexible and structured way; to upload, use, manipulate and analyze lists; to provide services for flexible retrieval of sequence segments  ...  InterMine (www.intermine.org) is a biological data warehousing system providing extensive automatically generated and configurable RESTful web services that underpin the web interface and can be re-used  ...  ACKNOWLEDGEMENT The authors would like to thank our users and collaborators for their continuing interest and support.  ... 
doi:10.1093/nar/gku301 pmid:24753429 pmcid:PMC4086141 fatcat:5s7obzx6gnevrj66v44mdodfdq

Understanding the Systems Biology of Pathogen Virulence Using Semantic Methodologies

David Rhee, Kevin Shieh, Julie Sullivan, Gos Micklem, Kami Kim, Aaron Golden
2016 2016 IEEE Tenth International Conference on Semantic Computing (ICSC)  
One promising solution is to apply semantic techniques on a self-consistent and implicitly correct ontological representation of these data types.  ...  The central problem remains empowering the scientific community to actually implement such an integration, across seemingly diverse data types and measurements.  ...  This work was also supported by the Wellcome Trust (Grant number 099133 to Dr. G. Micklem) and National Human Genome Research Institute (Grant Number: R01HG004834 to Dr. G. Micklem).  ... 
doi:10.1109/icsc.2016.33 dblp:conf/semco/RheeSSMKG16 fatcat:qgwc3e53wvd4bhgusjrmmgbyfm

Cross-species Conservation of context-specific networks

Robert Pesch, Ralf Zimmer
2016 BMC Systems Biology  
Results: The Cross-species Conservation framework (CroCo) provides a network-oriented view on the ENCODE regulatory data (CroCo network repository), convenient ways to access and browse networks and metadata  ...  Conclusion: CroCo adds an intuitive unifying view on the data from the ENCODE projects via a comprehensive repository of derived context-specific regulatory networks and enables flexible cross-context,  ...  Acknowledgments We would like to thank Madox Sesen for prototyping the network motif overlap functionality.  ... 
doi:10.1186/s12918-016-0304-1 pmid:27531214 pmcid:PMC4988053 fatcat:ogaz3qgpdrgcnoamwho2bcledq

ThaleMine: A Warehouse for Arabidopsis Data Integration and Discovery

Vivek Krishnakumar, Sergio Contrino, Chia-Yi Cheng, Irina Belyaeva, Erik S. Ferlanti, Jason R. Miller, Matthew W. Vaughn, Gos Micklem, Christopher D. Town, Agnes P. Chan
2016 Plant and Cell Physiology  
The warehoused data can be accessed by users via graphical interfaces, as well as programmatically via web-services.  ...  InterMine has been broadly adopted by the model organism research community including nematode, rat, mouse, zebrafish, budding yeast, the modENCODE project, as well as being used for human data.  ...  Acknowledgements We would like to thank the InterMine team at the University of Cambridge for their valuable input and continuous support over the course of development of ThaleMine, the TACC Technology  ... 
doi:10.1093/pcp/pcw200 pmid:28013278 fatcat:peu7pyxi5bcevkhk2xzue6uq44
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