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modMine: flexible access to modENCODE data
2011
Nucleic Acids Research
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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
2013
BMC Genomics
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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
2011
Database: The Journal of Biological Databases and Curation
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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
2012
Bioinformatics
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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
2015
Database: The Journal of Biological Databases and Curation
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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
2012
Database: The Journal of Biological Databases and Curation
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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
2014
Genetics
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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
2012
BMC Genomics
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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
2014
F1000Research
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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
2014
F1000Research
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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
2016
Zebrafish
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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
2014
Nucleic Acids Research
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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
2016
2016 IEEE Tenth International Conference on Semantic Computing (ICSC)
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2016 pre-print arXiv:1604.05189v1 fatcat:lktsltr6pfhgjl7ruenlghfbzi
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
2016
BMC Systems Biology
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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
2016
Plant and Cell Physiology
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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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