Jump to content

PATRIC: Difference between revisions

Add links
From Wikipedia, the free encyclopedia
Browse history interactively
← Previous editNext edit →
Content deleted Content added
VisualWikitext
mNo edit summary
Added information about Bacterial and Viral Bioinformatics Resource Center (BV-BRC), which now contains PATRIC.
Line 1: Line 1:
{{other uses|Patric (disambiguation)}}
{{other uses|Patric (disambiguation)}}
{{Advert|date=December 2021}}
{{Advert|date=December 2021}}
'''PATRIC'''<ref>{{cite journal |vauthors=Gillespie JJ, Wattam AR, Cammer SA, etal |title=PATRIC: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic species |journal=Infection and Immunity |volume=79 |issue=11 |pages=4286–98 |date=November 2011 |pmid=21896772 |pmc=3257917 |doi=10.1128/IAI.00207-11 }}</ref> (Pathosystems Resource Integration Center) is a bacterial [[bioinformatics]] website from the [[Bioinformatics Resource Centers|Bioinformatics Resource Center]]. It is an information system that integrates databases with various types of data about bacterial pathogens (transcriptomic, proteomic, structural, and biochemical) and with analysis tools. It is designed to support the biomedical research community's work on bacterial infectious diseases via these integrations of various pieces of pathogen information.
'''PATRIC'''<ref>{{cite journal |vauthors=Gillespie JJ, Wattam AR, Cammer SA, etal |title=PATRIC: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic species |journal=Infection and Immunity |volume=79 |issue=11 |pages=4286–98 |date=November 2011 |pmid=21896772 |pmc=3257917 |doi=10.1128/IAI.00207-11 }}</ref> (Pathosystems Resource Integration Center) was a bacterial [[bioinformatics]] website from the [[Bioinformatics Resource Centers|Bioinformatics Resource Center]], originally created in 2004.<ref>{{Cite journal |last=Davis |first=James J |last2=Wattam |first2=Alice R |last3=Aziz |first3=Ramy K |last4=Brettin |first4=Thomas |last5=Butler |first5=Ralph |last6=Butler |first6=Rory M |last7=Chlenski |first7=Philippe |last8=Conrad |first8=Neal |last9=Dickerman |first9=Allan |last10=Dietrich |first10=Emily M |last11=Gabbard |first11=Joseph L |last12=Gerdes |first12=Svetlana |last13=Guard |first13=Andrew |last14=Kenyon |first14=Ronald W |last15=Machi |first15=Dustin |date=2019-10-31 |title=The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities |url=https://doi.org/10.1093/nar/gkz943 |journal=Nucleic Acids Research |doi=10.1093/nar/gkz943 |issn=0305-1048 |pmc=PMC7145515 |pmid=31667520}}</ref> It has since been combined with the Influenza Research Database and the Virus Pathogen Database and Analysis Resource Center to create the Bacterial and Viral Bioinformatics Resource Center (BV-BRC).<ref>{{Cite journal |last=Olson |first=Robert D. |last2=Assaf |first2=Rida |last3=Brettin |first3=Thomas |last4=Conrad |first4=Neal |last5=Cucinell |first5=Clark |last6=Davis |first6=James J. |last7=Dempsey |first7=Donald M. |last8=Dickerman |first8=Allan |last9=Dietrich |first9=Emily M. |last10=Kenyon |first10=Ronald W. |last11=Kuscuoglu |first11=Mehmet |last12=Lefkowitz |first12=Elliot J. |last13=Lu |first13=Jian |last14=Machi |first14=Dustin |last15=Macken |first15=Catherine |date=2023-01-06 |title=Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR |url=https://pubmed.ncbi.nlm.nih.gov/36350631/ |journal=Nucleic Acids Research |volume=51 |issue=D1 |pages=D678–D689 |doi=10.1093/nar/gkac1003 |issn=1362-4962 |pmc=9825582 |pmid=36350631}}</ref> It is an information system that integrates databases with various types of data about bacterial pathogens (transcriptomic, proteomic, structural, and biochemical) with analysis tools. It is designed to support the biomedical research community's work on bacterial infectious diseases via these integrations of various pieces of pathogen information.


==Description==
==Description==
PATRIC is a project of Virginia Tech's [[Cyberinfrastructure]] Division and is funded by the National Institutes of Allergy and Infectious Diseases ([[NIAID]]), a component of the National Institutes of Health ([[NIH]]). PATRIC centralizes available bacterial phylogenomic data, proteomic data, and other various experiment pieces of data linked to specific pathogens from numerous sources.<ref name=Sobral2013>{{cite book |language=en |first1=Bruno |last1=Sobral |author2=Chunhong Mao |author3=Maulik Shukla |author4=Dan Sullivan |author5=Chengdong Zhang |chapter=Informatics-Driven Infectious Disease Research |title=Biomedical Engineering Systems and Technologies|isbn=9783642297526 |publisher=Springer Berlin |pages=3–11 |access-date=5 March 2022 |veditors=Fred A, Gamboa H, Filipe J |date=3 January 2013 |url=https://books.google.com/books?id=TP66BQAAQBAJ}}</ref> The PATRIC platform provides an interface for comprehensive [[comparative genomics]].
PATRIC was started as a project of Virginia Tech's [[Cyberinfrastructure]] Division and is funded by the National Institutes of Allergy and Infectious Diseases ([[NIAID]]), a component of the National Institutes of Health ([[NIH]]). PATRIC centralizes available bacterial phylogenomic data, proteomic data, and other various experiment pieces of data linked to specific pathogens from numerous sources.<ref name=Sobral2013>{{cite book |language=en |first1=Bruno |last1=Sobral |author2=Chunhong Mao |author3=Maulik Shukla |author4=Dan Sullivan |author5=Chengdong Zhang |chapter=Informatics-Driven Infectious Disease Research |title=Biomedical Engineering Systems and Technologies|isbn=9783642297526 |publisher=Springer Berlin |pages=3–11 |access-date=5 March 2022 |veditors=Fred A, Gamboa H, Filipe J |date=3 January 2013 |url=https://books.google.com/books?id=TP66BQAAQBAJ}}</ref> The PATRIC platform provides an interface for comprehensive [[comparative genomics]]. In 2019, the NIAID issued further funding to Dr. [[Rick Stevens]] at the [[University of Chicago]] for the Bioinformatics Resource Center, the current umbrella under which PATRIC is contained.<ref>{{Cite web |title=RePORT ⟩ RePORTER |url=https://reporter.nih.gov/project-details/10217942 |access-date=2023-12-01 |website=reporter.nih.gov}}</ref>

==Bacterial Organisms Covered in the PATRIC Database==
==Bacterial Organisms Covered in the PATRIC Database==
* [[Bacillus]]
* [[Bacillus]]

Revision as of 22:05, 1 December 2023

For other uses, see Patric (disambiguation).

PATRIC[1] (Pathosystems Resource Integration Center) was a bacterial bioinformatics website from the Bioinformatics Resource Center, originally created in 2004.[2] It has since been combined with the Influenza Research Database and the Virus Pathogen Database and Analysis Resource Center to create the Bacterial and Viral Bioinformatics Resource Center (BV-BRC).[3] It is an information system that integrates databases with various types of data about bacterial pathogens (transcriptomic, proteomic, structural, and biochemical) with analysis tools. It is designed to support the biomedical research community's work on bacterial infectious diseases via these integrations of various pieces of pathogen information.

Description

PATRIC was started as a project of Virginia Tech's Cyberinfrastructure Division and is funded by the National Institutes of Allergy and Infectious Diseases (NIAID), a component of the National Institutes of Health (NIH). PATRIC centralizes available bacterial phylogenomic data, proteomic data, and other various experiment pieces of data linked to specific pathogens from numerous sources.[4] The PATRIC platform provides an interface for comprehensive comparative genomics. In 2019, the NIAID issued further funding to Dr. Rick Stevens at the University of Chicago for the Bioinformatics Resource Center, the current umbrella under which PATRIC is contained.[5]

Bacterial Organisms Covered in the PATRIC Database

About Cyberinfrastructure Division and VBI

The CyberInfrastructure Division at VBI develops methods, infrastructure, and resources to help enable scientific discoveries in infectious disease research. The group applies the principles of cyberinfrastructure to integrate data, computational infrastructure, and people. CyberInfrastructure Division has developed public resources for curated, diverse molecular and literature data from various infectious disease systems, and implemented the processes, systems, and databases required to support them. It also conducts research by applying its methods and data to make discoveries of its own.

The Virginia Bioinformatics Institute (VBI) at Virginia Tech has a research platform centered on understanding the "disease triangle" of host-pathogen-environment interactions in plants, humans, and other animals.

See also

References

  1. ^ Gillespie JJ, Wattam AR, Cammer SA, et al. (November 2011). "PATRIC: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic species". Infection and Immunity. 79 (11): 4286–98. doi:10.1128/IAI.00207-11. PMC 3257917. PMID 21896772.
  2. ^ Davis, James J; Wattam, Alice R; Aziz, Ramy K; Brettin, Thomas; Butler, Ralph; Butler, Rory M; Chlenski, Philippe; Conrad, Neal; Dickerman, Allan; Dietrich, Emily M; Gabbard, Joseph L; Gerdes, Svetlana; Guard, Andrew; Kenyon, Ronald W; Machi, Dustin (2019-10-31). "The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities". Nucleic Acids Research. doi:10.1093/nar/gkz943. ISSN 0305-1048. PMC 7145515. PMID 31667520.{{cite journal}}: CS1 maint: PMC format (link)
  3. ^ Olson, Robert D.; Assaf, Rida; Brettin, Thomas; Conrad, Neal; Cucinell, Clark; Davis, James J.; Dempsey, Donald M.; Dickerman, Allan; Dietrich, Emily M.; Kenyon, Ronald W.; Kuscuoglu, Mehmet; Lefkowitz, Elliot J.; Lu, Jian; Machi, Dustin; Macken, Catherine (2023-01-06). "Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR". Nucleic Acids Research. 51 (D1): D678–D689. doi:10.1093/nar/gkac1003. ISSN 1362-4962. PMC 9825582. PMID 36350631. {{cite journal}}: no-break space character in |title= at position 110 (help)
  4. ^ Sobral B, Chunhong Mao, Maulik Shukla, Dan Sullivan, Chengdong Zhang (3 January 2013). "Informatics-Driven Infectious Disease Research". In Fred A, Gamboa H, Filipe J (eds.). Biomedical Engineering Systems and Technologies. Springer Berlin. pp. 3–11. ISBN 9783642297526. Retrieved 5 March 2022.
  5. ^ "RePORT ⟩ RePORTER". reporter.nih.gov. Retrieved 2023-12-01.
Retrieved from "https://en.wikipedia.org/w/index.php?title=PATRIC&oldid=1187860677"