Where can I access Virulence and Disease Data on the PATRIC site?
This data can be accessed under the “Diseases” tab on any PATRIC Organism landing page and presents an overview of integrated host-pathogen data from an infectious disease perspective. It is present for every taxon in PATRIC for which we have infectious disease data that is associated with either the taxon itself or any children taxa.
What Virulence and Disease Data are available and how are the data interactive?
There are three tabs located midway down a Disease Overview page: “Summary”, “Disease-Pathogen Visualization”, and “Disease Map”.
The Summary tab provides an overview of disease, pathogen, and gene information including:
- A list of PubMed literature specifically related to the associated disease. This list is collapsible by clicking the arrow in the header row. Articles may be accessed directly by clicking the associated PubMed ID.
- An Infectious Disease Overview table containing pathogens and their associated MeSH disease terms, links to tables of known virulence factors, and links to tables of associated human genes. From the Infectious Disease Overview table you may:
- Access the National Library of Medicine MeSH Descriptor Data by clicking on any MeSH Disease Term.
- Access a specific PATRIC Organism landing page by clicking on a Pathogen.
- Access a Virulence Disease table by clicking on a number within the Pathogen Virulence Genes column.
- The Virulence Genes tab of this table lists bacterial genes that have been shown to play a role in virulence. From here you can read general information about each gene, access the original entry in the Virulence Factor Database (VFDB), and find PATRIC homologs of a given gene.
- The Virulence Gene Homologs tab lists homologs of known virulence genes in related PATRIC species (i.e., organisms in the same genus). From this tab you can access PATRIC features for each gene.
- Access tables of human genes associated with each disease, including genetic and chemical evidence for the associations by clicking on a number within the Human Disease Genes columns.
- The Genetic Association Source (GAD) table lists human genes that have been shown to have some genetic association with the given infectious disease(s). From this table, you can get more information about the gene from NCBI or GeneCards, access the original database entry in the Genetic Association Database (GAD), and read the published study that reported the association.
- The Chemical Association (CTD) table lists human genes that have been shown to have some association with the given infectious disease(s) via chemcial treatment or exposure. From this table, you can get more information about the gene from NCBI or GeneCards, access the original database entry in the Comparative Toxicogenomics Database (CTD), and read the published study that reported the association.
- Note: All tables accessed via the Infectious Disease Overview may be sorted and downloaded as described in Feature Table FAQs.
The Disease-Pathogen Visualization tab provides an interactive, graphical image of the relationships between pathogens, diseases, virulence genes, and disease-associated host genes. Nodes and edges in the graph can be clicked to display more specific information, including links to external resources. Controls along the top of the image allow you to filter the graph, adjust the view and the layout, export the graph as either an image or a Cytoscape-compatible file, and access PATRIC FAQs. Controls along the bottom of the graph allow you to pan and zoom.
The Disease Map tab provides a real-time global view of recent reports of associated diseases geolocated on an interactive global map. More information on Diseases, Places, and Sources is available along the bottom of the map.
For more information, see the publication:
- 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].
What are the sources of the Virulence and Disease Data?
- Bacterial infectious disease names are from the National Library of Medicine 2011 Medical Subject Headings (MeSH). We restrict our consideration to two parent MeSH headings: Gram-Positive Infections, and Gram-Negative Infections.
- Mappings between pathogen and disease are assigned by manual curation of MeSH term definitions and online medical references.
- Pathogen virulence genes are from two sources:
- Curated virulence genes are retrieved from the Virulence Factor Database (VFDB).
- Homologs of curated virulence genes are provided by a genus-restricted BLASTP search ( minimum percent identity of 95%, minimum query coverage of 80%, and minimum subject coverage of 80%).
- Human genes that are associated with infectious disease are from two sources:
- Genetic associations come from the Genetic Association Database (GAD). GAD is a public resource that houses manually curated results of human genetic association studies related to complex diseases and disorders. Data in GAD are extracted from published literature on candidate gene investigations and Genome-Wide Association Studies (GWAS).
- Chemical associations come from the Comparative Toxicogenomics Database (CTD). CTD is a community-supported public resource that provides manually curated data from published literature describing cross-species chemical–gene/protein interactions and chemical– and gene–disease relationships.
- Geolocated reports of disease are provided by HealthMap. HealthMap is a freely accessible, automated electronic information system for monitoring, organizing, and visualizing reports of global disease outbreaks. It brings together disparate data sources to achieve a comprehensive view of the current global state of infectious diseases. PATRIC provides HealthMap results for watchlist pathogens by directly mapping pathogens to sets of disease-related terms.