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Automated Querying of Genome Databases

Peter Schattner
2007 PLoS Computational Biology  
Interactive Batch Database-Querying Batch queries of the Ensembl and UCSC Genome Databases are possible using the conventional database SQL [10] or using the Application Programmer Interfaces (APIs),  ...  Such queries can be addressed in a straightforward manner by batch-querying the genome databases. In contrast, they are essentially impossible to answer via interactive genome browsing.  ... 
doi:10.1371/journal.pcbi.0030001 pmid:17257048 pmcid:PMC1782033 fatcat:myarq5e5szhkjfuuswt3jye6z4

Querying Genomic Databases: Refining the Connectivity Map

Mark R. Segal, Hao Xiong, Henrik Bengtsson, Richard Bourgon, Robert Gentleman
2012 Statistical Applications in Genetics and Molecular Biology  
The aforementioned signature serves as a query which is applied to a customized database of (differential) gene expression experiments designed to elicit response to a wide range of drugs, across of spectrum  ...  Firstly, we develop new approaches to measuring closeness for the common scenario wherein the query constitutes an ordered list.  ...  The aforementioned signature serves as a query which is applied to a customized database of (differential) gene expression experiments designed to elicit response to a wide range of drugs, across of spectrum  ... 
doi:10.2202/1544-6115.1715 pmid:22499690 fatcat:citp7uzwozhird6cf3islftsum


2005 Proceedings of the 3rd Asia-Pacific Bioinformatics Conference  
Graph databases can support visualization of both queries and results by drawing on the broader field of graph visualization, and the visual paradigm is natural for scientists working in genomics.  ...  We have constructed a graph database system that supports visual queries and visualization of query result sets. Our system uses Java, XML, C++, CORAL, and MySQL to implement the GraphLog language.  ...  However, none of these genomic graph databases has a visual query mechanism.  ... 
doi:10.1142/9781860947322_0004 fatcat:4bybvphm4vaa7l4tof4klnykhq

Private and Efficient Query Processing on Outsourced Genomic Databases

Reza Ghasemi, Md. Momin Al Aziz, Noman Mohammed, Massoud Hadian Dehkordi, Xiaoqian Jiang
2017 IEEE journal of biomedical and health informatics  
In this paper, we propose a privacypreserving model for outsourcing genomic data to a cloud. The proposed model enables query processing while providing privacy protection of genomic databases.  ...  Privacy of the individuals is guaranteed by permuting and adding fake genomic records in the database. These techniques allow cloud to evaluate count and top-k queries securely and efficiently.  ...  ., genome sequence or sensitive attributes) and the query execution mechanism should be scalable to large databases. A.  ... 
doi:10.1109/jbhi.2016.2625299 pmid:27834660 pmcid:PMC5498255 fatcat:gbp3hki5kzh2hlnvsyqoziyb2a

Automatic query mapping among genomic databases: a pilot exploration

K H Cheung, P Nadkarni, P Miller, D G Shin
1998 Proceedings. AMIA Symposium  
As databases in the human genome project proliferate, it is important for users of one genomic database to identify similar or inconsistent data in other autonomously developed genomic databases.  ...  We describe an approach that allows a query issued against one database to be automatically mapped to an equivalent query against another structurally different database.  ...  INTRODUCTION In the field of genome science, where databases play a crucial role in its success, it is important for genome scientists to query databases (including their own) that are related to their  ... 
pmid:9929357 pmcid:PMC2232293 fatcat:5az5jrw4znd3tdm7qd7xigbfgu

The Burkholderia Genome Database: facilitating flexible queries and comparative analyses

G. L. Winsor, B. Khaira, T. Van Rossum, R. Lo, M. D. Whiteside, F. S. L. Brinkman
2008 Bioinformatics  
The Burkholderia Genome Database represents a model for such a database, providing a powerful, user-friendly search and comparative analysis interface that contains features not found in other genome databases  ...  As the genome sequences of multiple strains of a given bacterial species are obtained, more generalized bacterial genome databases may be complemented by databases that are focused on providing more information  ...  ACKNOWLEDGEMENTS We thank all Burkholderia genome projects. FSLB is a Michael Smith Foundation for Health Research (MSFHR) Scholar and a CIHR New Investigator. MDW received a MSFHR scholarship.  ... 
doi:10.1093/bioinformatics/btn524 pmid:18842600 pmcid:PMC2639269 fatcat:sfgndxph6fdgvepgo5ezgquixq

Cyclone: java-based querying and computing with Pathway/Genome databases

F. L. Fevre, S. Smidtas, V. Schachter
2007 Bioinformatics  
Cyclone objects can also be stored in a relational database CycloneDB. Queries can be written in SQL, and in an intuitive and concise object-oriented query language, Hibernate Query Language (HQL).  ...  Cyclone aims at facilitating the use of BioCyc, a collection of Pathway/Genome Databases (PGDBs). Cyclone provides a fully extensible Java Object API to analyze and visualize these data.  ...  BioCyc is a collection of 205 species-specific 'Pathway/Genome Databases' (PGDB) managed by the proprietary software called 'Pathway Tools'.  ... 
doi:10.1093/bioinformatics/btm107 pmid:17392333 fatcat:qm3z2w46rnf4leeum5f4ssqix4

A Ruby API to query the Ensembl database for genomic features

F. Strozzi, J. Aerts
2011 Bioinformatics  
The Ensembl database makes genomic features available via its Genome Browser. It is also possible to access the underlying data through a Perl API for advanced querying.  ...  A single Ruby API is used to access different releases of the Ensembl databases and is also able to query multi-species databases.  ...  F.S. created the Variation API and adapted the code for Ensembl Genomes multi-species databases. Both contributed to the manuscript.  ... 
doi:10.1093/bioinformatics/btr050 pmid:21278190 pmcid:PMC3065687 fatcat:hknkbeiyvnc2bju76yf4f7qomq

EPISODE: Efficient Privacy-PreservIng Similar Sequence Queries on Outsourced Genomic DatabasEs

Thomas Schneider, Oleksandr Tkachenko
2019 Proceedings of the 2019 ACM Asia Conference on Computer and Communications Security - Asia CCS '19  
In addition, we show that our algorithm scales for practical database sizes by querying a database that contains up to a million short sequences within a few minutes, and a database with hundreds of whole-genome  ...  ., to find their relatives in a genomic database.  ...  of the database is crucial in genome analyses [37] .  ... 
doi:10.1145/3321705.3329800 dblp:conf/ccs/0003T19 fatcat:jgwib57iavdwvogwv3pa3u5mpa

Efficient Query Processing on Genomic Database using Data-Parallel Logic Programming Language

Hideo Matsuda
1993 Genome Informatics Series  
This paper proposes a prototype system for querying genomic database based on data-parallel logic programming.  ...  The efficient access to genomic database is crucial, given enormous increase in sequence data.  ...  This work was supported in part by the Japan Ministry of Education, Science and Culture under Grant in Aid for Scientific Research on Priority Areas entitled "Genome Informatics" (No. 05254209).  ... 
doi:10.11234/gi1990.4.17 fatcat:zwkflqoc7fb5ji5vsccpdh2dna

Efficient querying of genomic databases for single-cell RNA-seq with gget [article]

Laura Luebbert, Lior Pachter
2022 bioRxiv   pre-print
tool and Python package that enables efficient querying of genomic databases. gget consists of a collection of separate but interoperable modules, each designed to facilitate one type of database querying  ...  AbstractMotivationA recurring challenge in interpreting single-cell RNA-seq data is the assessment of results in the context of existing genomic databases.  ...  databases directly from a command line or Python environment. gget consists of a collection of tools designed to perform the database querying required for single-cell RNA-seq data analysis in a single  ... 
doi:10.1101/2022.05.17.492392 fatcat:y2qft3qceza57j5j7q4ybrruyi

CIDB: Chlamydia Interactive Database for cross-querying genomics, transcriptomics and proteomics data

Yan Chen, Peter Timms, Yi-Ping Phoebe Chen
2007 Biomolecular Engineering  
The Chlamydia Interactive Database (CIDB) described here is the first database of its type that holds genomic, RT-PCR, microarray and proteomics data sets that can be cross-queried by researchers for patterns  ...  Combining the data of many research groups into a single database and cross-querying from different perspectives should enhance our understanding of the complex cell biology of these pathogens.  ...  data and other available genomics from loosely federated remote databases.  ... 
doi:10.1016/j.bioeng.2007.08.017 pmid:17913579 fatcat:6nqav5mnorgfdjxziy2qd2v4bi

Making High-level Queries on Diverse Genome Data: A Structured Genome Document Database System Based on GXML and GQL

Aaron Stokes, Hideo Matsuda, Akihiro Hashimoto
1999 Genome Informatics Series  
A powerful query language is introduced that exposes important biological relationships among the genome data.  ...  To address these problems, we propose a new type of genome database system.  ...  Acknowledgements •\ 185 This work was supported in part by CREST of JST (Japan Science and Technology) , and a Grantin-Aid "Genome Science" (08283103) for Scientific Research on Priority Areas from the  ... 
doi:10.11234/gi1990.10.176 fatcat:nw4h4jgv5fcspjdvp2epg7thqu

Co-expressed Pathways DataBase for Tomato: a database to predict pathways relevant to a query gene

Takafumi Narise, Nozomu Sakurai, Takeshi Obayashi, Hiroyuki Ohta, Daisuke Shibata
2017 BMC Genomics  
These databases usually provide users with a co-expression network and a list of strongly co-expressed genes for a query gene.  ...  The database allows users to predict pathways that are relevant to a query gene, which would help to infer gene functions.  ...  Availability of data and materials Co-expressed Pathways DataBase for Tomato is available at  ... 
doi:10.1186/s12864-017-3786-3 pmid:28583129 pmcid:PMC5460524 fatcat:fdizsadcfzbgfiyj3znayazkfm

A natural language interface plug-in for cooperative query answering in biological databases

Hasan M Jamil
2012 BMC Genomics  
query into a semantically equivalent structured query over the database.  ...  One of the many unique features of biological databases is that the mere existence of a ground data item is not always a precondition for a query response.  ...  This article has been published as part of BMC Genomics Volume 13 Supplement 3, 2012: Selected articles from the IEEE International Conference on Bioinformatics and Biomedicine 2011: Genomics.  ... 
doi:10.1186/1471-2164-13-s3-s4 pmid:22759613 pmcid:PMC3323828 fatcat:wox57tzw6bhjnfxgbzrj7b3e7y
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