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PATRIC, the bacterial bioinformatics database and analysis resource


NAR Molecular Biology Database Collection entry number 1000
Alice R. Wattam1, David Abraham1, Oral Dalay1, Terry L. Disz2, 3, Timothy Driscoll1, Joseph L. Gabbard1, 4, Roger Gough1, Deborah Hix1, Ronald Kenyon1, Dustin Machi1, Chunhong Mao1, Eric K. Nordberg1, Robert Olson2, 3, Ross Overbeek3, 5, Gordon D. Pusch5, Maulik Shukla1, Julie Schulman1, Rick L. Stevens2, 6, Daniel E. Sullivan1, Veronika Vonstein5, Andrew Warren1, Rebecca Will1, Meredith J.C. Wilson1, Hyun Seung Yoo1, Chengdong Zhang1, Yan Zhang1, Bruno W. Sobral1, 7
1 Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, 24060, United States of America 2 Computation Institute, University of Chicago, Chicago, Illinois, 60637, United States of America 3 Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, 60637, United States of America 4 Grado Department of Industrial & Systems Engineering, Virginia Tech, Blacksburg, Virginia, 24060, United States of America 5 Fellowship for Interpretation of Genomes, Burr Ridge, Illinois, 60527, United States of America 6 Computing, Environment, and Life Sciences, Argonne National Laboratory, Argonne, Illinois, 60637, United States of America 7 Nestlé Institute of Health Sciences SA, Campus EPFL, Quartier de L'innovation, Lausanne, Switzerland

Database Description

The Pathosystems Resource Integration Center (PATRIC) is the all-bacterial Bioinformatics Resource Center (BRC) (http://www.patricbrc.org). A joint effort by two of the original NIAID-funded BRCs[1,2], PATRIC provides researchers with an online resource that stores and integrates a variety of data types (e.g. genomics, transcriptomics, protein-protein interactions, 3D protein structures and sequence typing data) and associated metadata. Datatypes are summarized for individual genomes and across taxonomic levels. As of September 2013, there are more than 10,000 bacterial genomes available in PATRIC. All genomes in PATRIC are consistently annotated using RAST, the Rapid Annotations using Subsystems Technology[3] to facilitate comparative genomics analysis. Summaries of different data types are also provided for individual genes, as well as comparisons of different annotations. PATRIC provides a variety of ways for researchers to find data of interest and a private workspace where they can store both genome and gene groups along with their own private data. Both private and public data can be analyzed together using a suite of tools to perform comparative genomic or transcriptomic analysis. PATRIC also includes integrated information related to disease.

Recent Developments

PATRIC has recently expanded and integrated transcriptomic data for an initial set of pathogens with their respective genomes. As of this writing, PATRIC has 704 transcriptomic datasets across 65 bacterial genera that have been incorporated from GEO[4]. Another development is an end-to-end support for transcriptomic data analysis that allows researchers to stream expression and annotation data from the RNA-Rocket, an RNA-Seq analysis pipeline developed in a cross BRC project[7,8] and available at the Pathogen Portal (http://www.pathogenportal.org/); examine it in the PATRIC genome browser; and store it in their private workspace. This gives researchers the ability to bring their own data to PATRIC and analyze it along side the other integrated transcriptomic experiments.

Acknowledgements

This work was supported by the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Service (Contract No. HHSN272200900040C).

References

1. Snyder E, Kampanya N, Lu J, Nordberg EK, Karur H, et al. (2007) PATRIC: the VBI pathosystems resource integration center. Nucleic acids research 35: D401-D406. 2. McNeil LK, Reich C, Aziz RK, Bartels D, Cohoon M, et al. (2007) The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation. Nucleic acids research 35: D347-D353. 3. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, et al. (2008) The RAST Server: rapid annotations using subsystems technology. BMC genomics 9: 75. 4. Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, et al. (2013) NCBI GEO: archive for functional genomics data sets—update. Nucleic acids research 41: D991-D995. 5. Rustici G, Kolesnikov N, Brandizi M, Burdett T, Dylag M, et al. (2013) ArrayExpress update—trends in database growth and links to data analysis tools. Nucleic acids research 41: D987-D990. 6. Vizcaíno JA, Côté RG, Csordas A, Dianes JA, Fabregat A, et al. (2013) The Proteomics Identifications (PRIDE) database and associated tools: status in 2013. Nucleic acids research 41: D1063-D1069. 7. Aurrecoechea C, Barreto A, Brestelli J, Brunk BP, Cade S, et al. (2013) EuPathDB: The Eukaryotic Pathogen database. Nucleic acids research 41: D684-D691. 8. Megy K, Emrich SJ, Lawson D, Campbell D, Dialynas E, et al. (2012) VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics. Nucleic acids research 40: D729-D734.


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