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Cristina Aurrecoechea,
Ana Barreto,
John Brestelli,
Brian P. Brunk,
Elisabet V. Caler,
Steve Fischer,
Bindu Gajria,
Xin Gao,
Alan Gingle,
Gregory R. Grant, [......],
Wei Li,
Vishal Nayak,
Cary Pennington,
Deborah F. Pinney,
Brian Pitts,
David S. Roos,
Ganesh Srinivasamoorthy,
Christian J. Stoeckert Jr, Charles Treatman,
Haiming Wang
Nucleic Acids Research. 01/2011; 39:612-619.
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Steve Fischer,
Cristina Aurrecoechea,
Brian P Brunk,
Xin Gao,
Omar S Harb,
Eileen T Kraemer,
Cary Pennington, Charles Treatman,
Jessica C Kissinger,
David S Roos,
Christian J Stoeckert
[show abstract]
[hide abstract]
ABSTRACT: Web sites associated with the Eukaryotic Pathogen Bioinformatics Resource Center (EuPathDB.org) have recently introduced a graphical user interface, the Strategies WDK, intended to make advanced searching and set and interval operations easy and accessible to all users. With a design guided by usability studies, the system helps motivate researchers to perform dynamic computational experiments and explore relationships across data sets. For example, PlasmoDB users seeking novel therapeutic targets may wish to locate putative enzymes that distinguish pathogens from their hosts, and that are expressed during appropriate developmental stages. When a researcher runs one of the approximately 100 searches available on the site, the search is presented as a first step in a strategy. The strategy is extended by running additional searches, which are combined with set operators (union, intersect or minus), or genomic interval operators (overlap, contains). A graphical display uses Venn diagrams to make the strategy's flow obvious. The interface facilitates interactive adjustment of the component searches with changes propagating forward through the strategy. Users may save their strategies, creating protocols that can be shared with colleagues. The strategy system has now been deployed on all EuPathDB databases, and successfully deployed by other projects. The Strategies WDK uses a configurable MVC architecture that is compatible with most genomics and biological warehouse databases, and is available for download at code.google.com/p/strategies-wdk. Database URL: www.eupathdb.org.
Database The Journal of Biological Databases and Curation 01/2011; 2011:bar027. · 2.07 Impact Factor
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Cristina Aurrecoechea,
Ana Barreto,
John Brestelli,
Brian P Brunk,
Elisabet V Caler,
Steve Fischer,
Bindu Gajria,
Xin Gao,
Alan Gingle,
Greg Grant, [......],
Wei Li,
Vishal Nayak,
Cary Pennington,
Deborah F Pinney,
Brian Pitts,
David S Roos,
Ganesh Srinivasamoorthy,
Christian J Stoeckert, Charles Treatman,
Haiming Wang
[show abstract]
[hide abstract]
ABSTRACT: AmoebaDB (http://AmoebaDB.org) and MicrosporidiaDB (http://MicrosporidiaDB.org) are new functional genomic databases serving the amoebozoa and microsporidia research communities, respectively. AmoebaDB contains the genomes of three Entamoeba species (E. dispar, E. invadens and E. histolityca) and microarray expression data for E. histolytica. MicrosporidiaDB contains the genomes of Encephalitozoon cuniculi, E. intestinalis and E. bieneusi. The databases belong to the National Institute of Allergy and Infectious Diseases (NIAID) funded EuPathDB (http://EuPathDB.org) Bioinformatics Resource Center family of integrated databases and assume the same architectural and graphical design as other EuPathDB resources such as PlasmoDB and TriTrypDB. Importantly they utilize the graphical strategy builder that affords a database user the ability to ask complex multi-data-type questions with relative ease and versatility. Genomic scale data can be queried based on BLAST searches, annotation keywords and gene ID searches, GO terms, sequence motifs, protein characteristics, phylogenetic relationships and functional data such as transcript (microarray and EST evidence) and protein expression data. Search strategies can be saved within a user's profile for future retrieval and may also be shared with other researchers using a unique strategy web address.
Nucleic Acids Research 10/2010; 39(Database issue):D612-9. · 8.03 Impact Factor
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Cristina Aurrecoechea,
John Brestelli,
Brian P. Brunk,
Steve Fischer,
Bindu Gajria,
Xin Gao,
Alan Gingle,
Gregory R. Grant,
Omar S. Harb,
Mark Heiges, [......],
Vishal Nayak,
Cary Pennington,
Deborah F. Pinney,
David S. Roos,
Chris Ross,
Ganesh Srinivasamoorthy,
Christian J. Stoeckert Jr,
Ryan Thibodeau, Charles Treatman,
Haiming Wang
Nucleic Acids Research. 01/2010; 38:415-419.
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Martin Aslett,
Cristina Aurrecoechea,
Matthew Berriman,
John Brestelli,
Brian P. Brunk,
Mark Carrington,
Daniel P. Depledge,
Steve Fischer,
Bindu Gajria,
Xin Gao, [......],
Dhileep Sivam,
Deborah F. Smith,
Ganesh Srinivasamoorthy,
Christian J. Stoeckert Jr,
Sandhya Subramanian,
Ryan Thibodeau,
Adrian Tivey, Charles Treatman,
Giles Velarde,
Haiming Wang
Nucleic Acids Research. 01/2010; 38:457-462.
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Cristina Aurrecoechea,
John Brestelli,
Brian P Brunk,
Steve Fischer,
Bindu Gajria,
Xin Gao,
Alan Gingle,
Greg Grant,
Omar S Harb,
Mark Heiges, [......],
Vishal Nayak,
Cary Pennington,
Deborah F Pinney,
David S Roos,
Chris Ross,
Ganesh Srinivasamoorthy,
Christian J Stoeckert,
Ryan Thibodeau, Charles Treatman,
Haiming Wang
[show abstract]
[hide abstract]
ABSTRACT: EuPathDB (http://EuPathDB.org; formerly ApiDB) is an integrated database covering the eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. The most recent release of EuPathDB includes updates and changes affecting data content, infrastructure and the user interface, improving data access and enhancing the user experience. EuPathDB currently supports more than 80 searches and the recently-implemented 'search strategy' system enables users to construct complex multi-step searches via a graphical interface. Search results are dynamically displayed as the strategy is constructed or modified, and can be downloaded, saved, revised, or shared with other database users.
Nucleic Acids Research 11/2009; 38(Database issue):D415-9. · 8.03 Impact Factor
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Martin Aslett,
Cristina Aurrecoechea,
Matthew Berriman,
John Brestelli,
Brian P Brunk,
Mark Carrington,
Daniel P Depledge,
Steve Fischer,
Bindu Gajria,
Xin Gao, [......],
Dhileep Sivam,
Deborah F Smith,
Ganesh Srinivasamoorthy,
Christian J Stoeckert,
Sandhya Subramanian,
Ryan Thibodeau,
Adrian Tivey, Charles Treatman,
Giles Velarde,
Haiming Wang
[show abstract]
[hide abstract]
ABSTRACT: TriTrypDB (http://tritrypdb.org) is an integrated database providing access to genome-scale datasets for kinetoplastid parasites, and supporting a variety of complex queries driven by research and development needs. TriTrypDB is a collaborative project, utilizing the GUS/WDK computational infrastructure developed by the Eukaryotic Pathogen Bioinformatics Resource Center (EuPathDB.org) to integrate genome annotation and analyses from GeneDB and elsewhere with a wide variety of functional genomics datasets made available by members of the global research community, often pre-publication. Currently, TriTrypDB integrates datasets from Leishmania braziliensis, L. infantum, L. major, L. tarentolae, Trypanosoma brucei and T. cruzi. Users may examine individual genes or chromosomal spans in their genomic context, including syntenic alignments with other kinetoplastid organisms. Data within TriTrypDB can be interrogated utilizing a sophisticated search strategy system that enables a user to construct complex queries combining multiple data types. All search strategies are stored, allowing future access and integrated searches. 'User Comments' may be added to any gene page, enhancing available annotation; such comments become immediately searchable via the text search, and are forwarded to curators for incorporation into the reference annotation when appropriate.
Nucleic Acids Research 10/2009; 38(Database issue):D457-62. · 8.03 Impact Factor
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Cristina Aurrecoechea,
John Brestelli,
Brian P. Brunk,
Jennifer Dommer,
Steve Fischer,
Bindu Gajria,
Xin Gao,
Alan Gingle,
Gregory R. Grant,
Omar S. Harb, [......],
Wei Li,
John A. Miller,
Vishal Nayak,
Cary Pennington,
Deborah F. Pinney,
David S. Roos,
Chris Ross,
Christian J. Stoeckert Jr, Charles Treatman,
Haiming Wang
Nucleic Acids Research. 01/2009; 37:539-543.
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Cristina Aurrecoechea,
John Brestelli,
Brian P. Brunk,
Jane M. Carlton,
Jennifer Dommer,
Steve Fischer,
Bindu Gajria,
Xin Gao,
Alan Gingle,
Gregory R. Grant, [......],
Hilary G. Morrison,
Vishal Nayak,
Cary Pennington,
Deborah F. Pinney,
David S. Roos,
Chris Ross,
Christian J. Stoeckert Jr,
Steven Sullivan, Charles Treatman,
Haiming Wang
Nucleic Acids Research. 01/2009; 37:526-530.
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Cristina Aurrecoechea,
John Brestelli,
Brian P Brunk,
Jennifer Dommer,
Steve Fischer,
Bindu Gajria,
Xin Gao,
Alan Gingle,
Greg Grant,
Omar S Harb, [......],
Wei Li,
John A Miller,
Vishal Nayak,
Cary Pennington,
Deborah F Pinney,
David S Roos,
Chris Ross,
Christian J Stoeckert, Charles Treatman,
Haiming Wang
[show abstract]
[hide abstract]
ABSTRACT: PlasmoDB (http://PlasmoDB.org) is a functional genomic database for Plasmodium spp. that provides a resource for data analysis and visualization in a gene-by-gene or genome-wide scale. PlasmoDB belongs to a family of genomic resources that are housed under the EuPathDB (http://EuPathDB.org) Bioinformatics Resource Center (BRC) umbrella. The latest release, PlasmoDB 5.5, contains numerous new data types from several broad categories--annotated genomes, evidence of transcription, proteomics evidence, protein function evidence, population biology and evolution. Data in PlasmoDB can be queried by selecting the data of interest from a query grid or drop down menus. Various results can then be combined with each other on the query history page. Search results can be downloaded with associated functional data and registered users can store their query history for future retrieval or analysis.
Nucleic Acids Research 11/2008; 37(Database issue):D539-43. · 8.03 Impact Factor
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Cristina Aurrecoechea,
John Brestelli,
Brian P Brunk,
Jane M Carlton,
Jennifer Dommer,
Steve Fischer,
Bindu Gajria,
Xin Gao,
Alan Gingle,
Greg Grant, [......],
Hilary G Morrison,
Vishal Nayak,
Cary Pennington,
Deborah F Pinney,
David S Roos,
Chris Ross,
Christian J Stoeckert,
Steven Sullivan, Charles Treatman,
Haiming Wang
[show abstract]
[hide abstract]
ABSTRACT: GiardiaDB (http://GiardiaDB.org) and TrichDB (http://TrichDB.org) house the genome databases for Giardia lamblia and Trichomonas vaginalis, respectively, and represent the latest additions to the EuPathDB (http://EuPathDB.org) family of functional genomic databases. GiardiaDB and TrichDB employ the same framework as other EuPathDB sites (CryptoDB, PlasmoDB and ToxoDB), supporting fully integrated and searchable databases. Genomic-scale data available via these resources may be queried based on BLAST searches, annotation keywords and gene ID searches, GO terms, sequence motifs and other protein characteristics. Functional queries may also be formulated, based on transcript and protein expression data from a variety of platforms. Phylogenetic relationships may also be interrogated. The ability to combine the results from independent queries, and to store queries and query results for future use facilitates complex, genome-wide mining of functional genomic data.
Nucleic Acids Research 10/2008; 37(Database issue):D526-30. · 8.03 Impact Factor
