host_pathogen_eid2 — Host-pathogen interactions and pathogen locations (EID2, 1950-2012)

Description

Networks of interactions between species, where one (the "cargo") is likely to be a pathogen, parasite or other organism carried by the other (the "carrier", e.g. a host), and of the countries where species were found, from the ENHanCEd Infectious Diseases database (EID2) of Wardeh et al. The interactions were automatically extracted from the metadata of the NCBI Nucleotide sequence database (the organism of a sequence and its host) and from the PubMed literature database (publications mentioning both species, or a species and a location), based on evidence published between 1950 and 2012. Organism names were disambiguated with the NCBI Taxonomy database, and only organisms identified at the species or subspecies level are included; locations were disambiguated using GeoNames. The datasets were extracted from EID2 in 2015.

species: directed network of species, where an edge goes from a cargo species to a carrier species. A species may appear both as a cargo and a carrier. A few cargo-carrier pairs appear more than once in the data, and are kept as parallel edges.
locations: bipartite network of species and countries, where an edge connects a species to a country where it was found. Some records refer to a region (first-level administrative division) of the country, in which case it is stored as an edge property, so that a species and country can be connected by more than one edge.

The networks have the following properties:

species nodes: name, the species name; cargo_class and carrier_class, the taxonomic classification of the species when it appears as a cargo (e.g. "Bacteria", "Virus", "Helminth") or as a carrier (e.g. "Human", "Domestic", "Mammal", "Higher Plants"), or empty if the species does not appear in that role. The carrier category "Domestic" comprises 46 species of domesticated mammals and birds in Europe, so that a few species have different cargo and carrier classifications.
locations nodes: name, the species or country name; is_country, whether the node is a country (otherwise a species); classification, the taxonomic classification of the species (empty for countries).
Edges (both networks): sequences, the number of nucleotide sequences supporting the interaction; publications, the number of PubMed publications supporting the interaction. The lists of sequence and publication identifiers in the source data are not included.
locations edges: region, the region of the country (empty if the record refers to the country as a whole).

Tags

Biological Public Health Weighted Metadata Multigraph

Citation

M. Wardeh, C. Risley, M. K. McIntyre, C. Setzkorn, M. Baylis, "Database of host-pathogen and related species interactions, and their global distribution." Scientific Data 2, 150049 (2015) 10.1038/sdata.2015.49 Sci-Hub

Upstream URL OK

https://doi.org/10.1038/sdata.2015.49

Upstream license

Creative Commons Attribution 4.0 International (CC BY 4.0), https://creativecommons.org/licenses/by/4.0/

Networks

Tip: click on a column header to sort the list, or hover over it for a description.

Column legend

$\left<k\right>$: Mean degree
$\sigma_k$: Standard deviation of the degrees
$\lambda_h$: Largest eigenvalue of the Hashimoto (non-backtracking) matrix
$\tau$: Random walk mixing time
$r$: Degree assortativity
$c$: Global clustering coefficient
$\oslash$: (Pseudo-) diameter
$S$: Relative size of the largest component
NPs: Node properties
EPs: Edge properties

Name	Nodes	Edges	$\left<k\right>$	$\sigma_k$	$\lambda_h$	$\tau$	$r$	$c$	$\oslash$	$S$	Kind	Mode	NPs	EPs	gt	GraphML	GML	csv
species	15,024	22,515	1.50	16.19	31.56	542.10	-0.07	0.00	24	0.72	Directed	Unipartite	name cargo_class carrier_class	sequences publications	196 KiB	291 KiB	283 KiB	265 KiB
locations	72,775	157,148	4.32	111.64	86.95	19.21	-0.31	0.00	8	1.00	Undirected	Bipartite	name is_country classification	sequences publications region	1.0 MiB	1.8 MiB	1.8 MiB	1.8 MiB