PATRIC 2.0

Ammerman NC, Gillespie JJ, Neuwald AF, Sobral BW, Azad AF. (2009) A typhus group-specific protease defies reductive evolution in rickettsiae. J. Bacteriol.   doi:  10.1128/JB.01077-09.  PMID: 19820087.  PMCID: PMC2786609.

Ananiadou Sophia, Dan Sullivan, William Black, Gina-Anne Levow, Joseph J. Gillespie,
Chunhong Mao, Sampo Pyysalo, BalaKrishna Kolluru, Junichi Tsujii, Bruno Sobral. (2011). Named Entity Recognition for Bacterial Type IV Secretion Systems. PLoS ONE. March 29, 2011.  doi:10.1371/journal.pone.0014780. PMID: 21468321.  PMCID: PMC3066171.

Dreher-Lesnick SM, Ceraul SM, Lesnick SC, Gillespie JJ, Anderson JM, Jochim RC, Valenzuela JG, Azad AF. (2010) Analysis of Rickettsia typhi-infected and uninfected cat flea (Ctenocephalides felis) midgut cDNA libraries: deciphering molecular pathways involved in host response to R. typhi infection. Insect Mol. Biol.  doi: 10.1111/j.1365-2583.2009.00978.x.  PMID: 20017753.  PMCID: PMCID: PMC3179627.

Driscoll Timothy, Joseph L. Gabbard, Chunhong Mao, Oral Dalay, Maulik Shukla, Clark C. Freifeld, Anne Gatewood Hoen, John S. Brownstein JS, Bruno W. Sobral. Integration and visualization of host-pathogen data related to infectious diseases. Bioinformatics. 2011 Jun 27. doi: 10.1093/bioinformatics/btr391. PMID: 21712250. PMCID: PMC3150046 [Available on 2012/8/15].

Dyer MD, Neff C, Dufford M, Rivera CG, Shattuck D, et al. 2010 The Human-Bacterial Pathogen Protein Interaction Networks of Bacillus anthracis, Francisella tularensis, and Yersinia pestis. PLoS ONE 5(8): e12089. doi:10.1371/journal.pone.0012089. PMID: 20711500.  PMCID: PMC2918508.

Gillespie, J.J.*, Joardar, V.*, Williams, K.P., Driscoll, T., Hostetler, J.B., Nordberg, E.K., Shukla, M., Walenz, B., Hill, C.A., Nene, V.M., Azad, A.F., Sobral, B.W., Caler, E. (2012).  A Rickettsia genome overrun by mobile genetic elements provides insight into the acquisition of genes characteristic of an obligate intracellular lifestyle.  Journal of Bacteriology 194: 376-394. *equal author contribution.  doi: 10.1128/ JB.06244-11.  PMID: 22056929. PMCID: PMC3256634.

Gillespie Joseph J. , Alice R. Wattam, Stephen A. Cammer, Joseph Gabbard, Maulik P. Shukla, Oral Dalay, Timothy Driscoll, Deborah Hix, Shrinivasrao P. Mane, Chunhong Mao, Eric K. Nordberg, Mark Scott, Julie R. Schulman, Eric E. Snyder, Daniel E. Sullivan, Chunxia Wang, Andrew Warren, Kelly P. Williams, Tian Xue, Hyun Seung Yoo, Chengdong Zhang, Yan Zhang, Rebecca Will, Ronald W. Kenyon, and Bruno W. Sobral (2011). “PATRIC: The Comprehensive Bacterial Bioinformatics Resource with a Focus on Human Pathogenic Species”
Infect. Immun 79 (11): 4286-98. doi:10.1128/IAI.00207-11.   PMC 3257917.   PMID 21896772.

Gillespie JJ, Brayton KA, Williams KP, Diaz MA, Brown WC, Azad AF, Sobral BW. (2010) Phylogenomics reveals a diverse Rickettsiales type IV secretion system. Infect. Immun.  doi:  10.1128/IAI.01384-09.  PMID: 20176788.  PMCID: PMC2863512.

Pyysalo Sampo, Tomoko Ohta, Rafal Rak, Dan Sullivan, Chunhong Mao, Chunxia Wang, Bruno Sobral, Jun’ichi Tsujii, Sophia Ananiadou (2011). Overview of the Infectious Diseases (ID) task of BioNLP Shared Task 2011. Proceedings of BioNLP Shared Task 2011 Workshop, pages 26–35, Portland, Oregon, USA, 24 June, 2011. (View Full Paper at Association of Computational Linguistics Website).

Pyysalo Sampo, Tomoko Ohta, Han-Cheol Cho, Dan Sullivan, Chunhong Mao, Bruno Sobral,
Jun’ichi Tsujii and Sophia Ananiadou (2010). Towards Event Extraction from Full Texts on Infectious Diseases. Proceedings of the 2010 Workshop on Biomedical Natural Language Processing, ACL
2010, pages 132–140, Uppsala, Sweden, 15 July 2010.(View Full Paper at the Association of Computational Linguistics Website).

Rafal Rak, Andrew Rowley, William Black, and Sophia Ananiadou (2012). “Argo: an integrative, interactive, text mining-based workbench supporting curation”  Oxford Journals. Published online 2012 Feburary 13.  doi:10.1093/database/bas010. PMID: 22434844. PMC 3308166.

Sobral, B. and A. Wattam (2011). Comparative genomics and phylogenomics of the Brucella. Book chapter in “Brucella: Molecular Microbiology and Genetics”. I. L.-G. D. O’Callaghan, Horizon Scientific Press.

Sullivan DE, Gabbard JL, Shukla M, Sobral B. (2010) Data integration for dynamic and sustainable systems biology resources: challenges and lessons learned. Chem. Biodivers.  doi:  10.1002/cbdv.200900317.  PMID: 20491070.  PMCID: PMC2894471.

Sutten EL, Norimine J, Beare PA, Heinzen RA, Lopez JE, Morse K, Brayton KA, Gillespie JJ, Brown WC. (2010) Anaplasma marginale type IV secretion system proteins VirB2, VirB7, VirB11, and VirD4 are immunogenic components of a protective bacterial membrane vaccine. Infect. Immun.  doi:  10.1128/IAI.01207-09.  PMID: 20065028.  PMCID: PMC2825951.

Williams KP, Gillespie JJ, Sobral BW, Nordberg EK, Snyder EE, Shallom JM, Dickerman AW. (2010) Phylogeny of gammaproteobacteria. J. Bacteriol.  doi:  10.1128/JB.01480-09.  PMID: 20207755.  PMCID: PMC2863478.

PATRIC 1.0

Snyder EE, Kampanya N, Lu J, Nordberg EK, Karur HR, Shukla M, Soneja J, Tian Y, Xue T, Yoo H, Zhang F, Dharmanolla C, Dongre NV, Gillespie JJ, Hamelius J, Hance M, Huntington KI, Jukneliene D, Koziski J, Mackasmiel L, Mane SP, Nguyen V, Purkayastha A, Shallom J, Yu G, Guo Y, Gabbard J, Hix D, Azad AF, Baker SC, Boyle SM, Khudyakov Y, Meng XJ, Rupprecht C, Vinje J, Crasta OR, Czar MJ, Dickerman A, Eckart JD, Kenyon R, Will R, Setubal JC, Sobral BW. (2007) PATRIC: the VBI PathoSystems Resource Integration Center. Nucleic Acids Res. doi:  10.1093/nar/gkl858.  PMID: 17142235.  PMCID: PMC1669763.

>> Click here to take the PATRIC survey.

• The guide provides the list of resistant, susceptible and humanized mouse models used in the infection studies.
• Pathogens (bacteria, eukaryotic pathogens and viruses) are linked out directly to their corresponding BRC websites (PATRIC, EuPathDB, ViPR and IRD).
• Mouse strains selected for the pathogen infection studies are linked out to the JAX mice database for detailed mouse strain information and purchasing information (if any).
• The PubMed and Mouse Genome Informatics (MGI) references are provided.

Abstract

Curation of biomedical literature is often supported by the automatic analysis of textual content that generally involves a sequence of individual processing components. Text mining (TM) has been used to enhance the process of manual biocuration, but has been focused on specific databases and tasks rather than an environment integrating TM tools into the curation pipeline, catering for a variety of tasks, types of information and applications. Processing components usually come from different sources and often lack interoperability. The well established Unstructured Information Management Architecture is a framework that addresses interoperability by defining common data structures and interfaces. However, most of the efforts are targeted towards software developers and are not suitable for curators, or are otherwise inconvenient to use on a higher level of abstraction. To overcome these issues we introduce Argo, an interoperable, integrative, interactive and collaborative system for text analysis with a convenient graphic user interface to ease the development of processing workflows and boost productivity in labour-intensive manual curation. Robust, scalable text analytics follow a modular approach, adopting component modules for distinct levels of text analysis. The user interface is available entirely through a web browser that saves the user from going through often complicated and platform-dependent installation procedures. Argo comes with a predefined set of processing components commonly used in text analysis, while giving the users the ability to deposit their own components. The system accommodates various areas and levels of user expertise, from TM and computational linguistics to ontology-based curation. One of the key functionalities of Argo is its ability to seamlessly incorporate user-interactive components, such as manual annotation editors, into otherwise completely automatic pipelines. As a use case, we demonstrate the functionality of an in-built manual annotation editor that is well suited for in-text corpus annotation tasks.

1. Mycobacterium tuberculosis H37RvAE
2. Mycobacterium tuberculosis H37Rv (Broad)
3. Mycobacterium tuberculosis H37RvCO
4. Mycobacterium tuberculosis H37RvHA
5. Mycobacterium tuberculosis H37RvJO
6. Mycobacterium tuberculosis H37RvLP
7. Mycobacterium tuberculosis H37RvMA
8. Mycobacterium tuberculosis KZN 4207 (Broad)
9. Mycobacterium tuberculosis NCGM2209
10. Mycobacterium tuberculosis OSDD071
11. Mycobacterium tuberculosis OSDD504
12. Mycobacterium tuberculosis OSDD518

“Bioinformatics.org has announced the finalists in the 2012 Benjamin Franklin Award.

The Benjamin Franklin Award for Open Access in the Life Sciences is a humanitarian/bioethics award presented annually by Bioinformatics.org an individual who has, in his or her practice, promoted free and open access to the materials and methods used in the life sciences. Winners are chosen by voting members of Bioinformatics.org.

The 2012 winner will be announced at the Tenth Anniversary Bio-IT World Conference and Expo on April 25 in Boston. For more details, visit http://www.bio-itworldexpo.com/. “

• See list of finalists and read full article at:  http://www.bio-itworld.com/2012/02/28/2012-benjamin-franklin-award-finalists-named.html

• Find out more about the Benjamin Franklin Award and vote at:  http://www.bioinformatics.org/franklin/vote/2012/

Above Quote from Bio-IT World article. 2012 Benjamin Franklin Award Finalists Named. Accessed 28 Feb 2012 http://www.bio-itworld.com/2012/02/28/2012-benjamin-franklin-award-finalists-named.html

The workshop was hosted by Texas A&M Health Science Center .   Topics included:

What PATRIC Offers:

• Consistent annotations across all sequenced bacterial species from GenBank.

• Searches based on taxonomy, gene name, locus tag, protein function/families, pathways, EC numbers, GO terms, and more.

• Data and analysis results are free and typically downloadable.

• Organism summaries; pre-sorted PubMed articles; interactive phylogenetic trees; virulence and disease information, and experimental data including, transcriptomics, proteomics, protein structure, and protein-protein interactions.

• Numerous interactive visualizations for genome browsing, multi-genome comparisons, pathway comparisons, protein family comparisons, phylogenetic trees with coupled MSAs, 3D protein structures, and feature group comparisons.

For event details see Texas PATRIC workshop flyer.

If you have a suggestion for a future workshop topic and/or location, please send it to us via the “contact us” link at the bottom of this page.