Pathogen Portal

Image map with pictures of organisms representing five Bioinformatics Resource Centers


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About Pathogen Portal

Pathogen Portal is a repository linking to the Bioinformatics Resource Centers (BRCs) sponsored by the National Institute of Allergy and Infectious Diseases (NIAID) and maintained by The Virginia Bioinformatics Institute. The BRCs are providing web-based resources to scientific community conducting basic and applied research on organisms considered potential agents of biowarfare or bioterrorism or causing emerging or re-emerging diseases.

Systems Architecture for the Pathogen Portal is available at https://github.com/cidvbi/PathogenPortal/wiki

About the Bioinformatics Resource Centers

What services are provided?

The Bioinformatics Resource Centers (BRCs) for Infectious Diseases program, a continuation and expansion of a program initiated in 2004, consists of five centers, each specializing in a different group of pathogens. Pathogens include, but are not limited to, those in the NIAID Category A-C Priority Pathogen lists for biodefense research, and pathogens causing emerging/reemerging infectious diseases. The groups of pathogens are:

All bacterial species
All viral families
All eukaryotic pathogen species
Invertebrate vectors of human pathogens
Influenza virus

Each Center:

Stores, updates, integrates and displays genome sequence data and annotation, as well as many research data types, including functional genomics, proteomics, metagenomics and other “-omics” data, epidemiology, surveillance, population genetics, genotype/phenotype association data, expression data, antimicrobial resistance data, antigenic data, basic research and clinical data.
Makes available analytical resources, bioinformatics tools and services for data analysis.
Supplies experimental protocols and other relevant metadata.
Offers bioinformatics training at the BRCs’ sites or at the requesting institution or laboratory.
Partners with infectious disease research communities through the establishment of “Driving Biological Projects” to provide experimental biology laboratories with bioinformatics services.

Where are services provided?

Five centers, each specializing in a different group of pathogens including, but not limited to, NIAID Category A-C Priority Pathogen lists for biodefense research, and pathogens causing emerging/reemerging infectious diseases, provide data, tools and services related to the above mentioned groups of pathogens.

In addition, 24-hour annotation services for bacterial genomes and metagenomics datasets are freely available respectively at http://rast.nmpdr.org/ and http://metagenomics.nmpdr.org/.

Access

Data, bioinformatics tools and services provided by the five BRCs are freely and publicly available to the scientific community through user-friendly web interfaces. The BRCs Pathogen Portal will promote interoperability among the BRCs and with other bioinformatics resources.

The experimental data and information generated by the Driving Biological Projects will also be made accessible to the broad scientific community through the individual BRCs and/or the BRCs Pathogen Portal. Such information is expected to support or improve the annotation of the genome, proteome and metabolome of the targeted pathogens.

Bioinformatics training opportunities are available at no cost upon request to the centers.

As of January 1, 2010, all data and information formerly available through the Administrative Resource Center for Biodefense Proteomics Research web site are now available as part of the BRCs Pathogen Portal.

Related Resources and Information

About Our NIAID-Funded Friends

The BRCs work collaboratively with other NIAID-funded bioinformatics resources to ensure that we provide integrated access to data generated and resources provided. The projects that we work with include:

Genome Sequencing Centers for Infectious Diseases
Structural Genomics Centers for Infectious Diseases
BEI Resources
Systems Biology for Infectious Disease Research

The Genome Sequencing Centers for Infectious Diseases (GSCID)

Many of the genomes and their metadata available at the BRCs come from the GSCs. The GSCs provide services for rapid and cost-efficient production of high-quality, genome sequences and high-throughput genotyping of NIAID Category A, B, and C priority pathogens, microorganisms responsible for emerging and re-emerging infectious diseases and their hosts, related organisms, clinical isolates, and invertebrate vectors of infectious diseases.

Read more about the application process if you are interested in requesting DNA sequencing, assembly, primary annotation, and analysis of a specific microorganism, group of microorganisms, or an invertebrate vector of infectious disease.

For more information about projects conducted by the GSCs, visit the individual Centers at

Structural Genomics Centers for Infectious Diseases

The Structural Genomics Centers for Infectious Diseases apply state-of-the-art, high-throughput structural biology technologies to characterize the three dimensional (3-D) atomic structure of targeted proteins from pathogens in theNIAID priority lists . These targeted proteins are those with an important biological role or potential targets for vaccine and drug development.

The Centers provide the research community with:

Experimental 3-D protein structures
Sequence-verified clones are made available through the BEI Resources Repository (BEI) . More will be added periodically.

The scientific community can make requests to the Centers to determine the structures of proteins of interest belonging to the targeted pathogens. For more information about the structures solved or current targets, visit the individual Centers at

For example, at PATRIC , NIAID’s bacteria BRC, you can see bacterial structures generated by the Centers, as well as make a request to the Centers for proteins at PATRIC that don’t currently have a structure.

The Biodefense and Emerging Infections Research Resources Repository (BEI Resources)

BEI Resources was established by NIAID to provide reagents, tools and information for studying Category A, B, and C priority pathogens, emerging infectious disease agents, non-pathogenic microbes, and other microbiological materials of relevance to the research community. BEI Resources acquires, authenticates, and produces reagents that scientists need to carry out basic research and develop improved diagnostic tests, vaccines, and therapies. By centralizing these functions within BEI Resources, access to and use of these materials in the scientific community is monitored and quality control of the reagents is assured.

In addition to supplying the infectious disease community with materials, BEI Resources also encourages and supports the deposit of materials from researchers and institutions. Depositing materials with BEI Resources has many advantages to the researcher and the research community, including secure storage and community access and distribution, all while protecting the intellectual property rights of the depositor.

Clones generated by the Structural Genomics Centers for Infectious Disease can be found at

http://www.beiresources.org/tabid/1901/stabid/1901/CollectionLinkID/10/Default.aspx.

As an example, NIAID’s Eukaryotic Pathogen Database BRC, EuPathDB, supports queries to the MR4 Malaria Resource Center located at BEI to identify genes based on reagent availability.

Systems Biology for Infectious Disease Research

The NIAID program in Systems Biology for Infectious Diseases Research utilizes a combination of computational and experimental methodologies to conduct research projects to analyze, identify, quantify, model, and predict the overall dynamics of the network of cellular molecular components of microbial organisms and their interactions with the host cells. The knowledge generated from the research projects, including research data, analytical software tools, computational models, experimental protocols, and reagents, is widely disseminated to the scientific community through publicly accessible databases and reagent repositories. The research findings will provide a deeper understanding of the overall complexity of the biological, biochemical and biophysical molecular processes in microbial organisms as well as how the molecular events within the pathogen lead to the initiation and progression of infectious disease.

There are two viral centers producing data:

Systems Influenza (and click on Data on the top navigation bar) working to develop a detailed transcriptional network model of the interaction between the influenza virus and innate immune cells in vivo.
Systems Virology Center focusing on the 2009 pandemic H1N1 influenza virus, and two NIAID priority pathogens, H5N1 avian influenza virus and severe acute respiratory syndrome coronavirus (SARS-CoV)

They are collaborating with the ViPR (virus) and IRD (influenza) BRCs to present the Systems Biology data to the viral research communities.

Two bacterial data centers also producing such data are:

Systems Biology for EnteroPathogens using iterative and complementary computational and experimental “omics” methodologies to analyze, identify, quantify, model, and ultimately predict the overall molecular processes involved in the pathogenesis of Salmonella and Yersinia species in macrophages.
TB Systems Biology is experimentally mapping and computationally modeling the molecular pathways of M. tuberculosis under conditions relevant to TB pathogenesis by performing systematic profiling using ChIP-seq, transcriptomics, proteomics, glycomics, metabolomics, and lipidomics during both in vitro and in vivo growth.

About Our Non-NIAID-Funded Friends