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An R package for working with the Ecological Database of the World's Insect Pathogens (EDWIP)

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insectDisease

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insectDisease: Programmatically access insect disease data from the Ecological Database of the World's Insect Pathogens (EDWIP)

See published Software Note in Ecography: (available here) See preprint (available here)

This is a database of known pathogens of many species of insects and other arthropods. This database was designed by David Onstad, and first described in Braxton et al (2003). The database is unique in that in addition to host-parasite associations that occur in nature, it also contains some true host absences: records of instances where a given host species was inoculated with a pathogen and found not to be susceptible to it. This database also contains a large amount of ecological data on hosts and parasites. Here, we document and preserve these data as an R package, also providing csv flatfiles in the csv folder.

Data are available programmatically through R or can be downloaded from the csv folder and used outside of R. The data consist of a set of files that maintain the original structure of the EDWIP data resource, with the main files serving to detail the interactions between insect hosts and nematode (?nematode or csv/nematode.csv), viral ((?viruses or csv/viruses.csv) and non-viral pathogens such as bacteria and protozoans (?nvpassoc or csv/nvpassoc.csv). There are also data on negative associations, which are failed inoculation attempts (?negative or csv/negative.csv) and represent "true zeros", which are rare data. Other information on citations (assocref, citation, viraref and noassref) are provided as well as host (hosts) and pathogne (pathogen) trait data. Cached versions of host and pathogen taxonomy are also included (hostTaxonomy and pathTaxonomy) and will be updated (along with the taxonomic information within each data product) with every release of the data.


The Data

hosts

column name description
RecordNo Sequence from 1:nrow(hosts)
DateEntered Date of initial data entry
Habitat Habitat of host
HostSpecies Host species
Synonyms Other names for the host species
Food What does the host eat?
genYr Number of generations per year
CommonName Host common name
ProvinceI Canadian provinces where host has been found.
InsectStatus Is the insect a pest, beneficial, endangered, unknown? Factor variable with 7 unique values
ModificationDate Modification date of entry
InCanada Citations for presence/absence of host in Canada. Numeric indices can be related to the citations in the citations.rda data file. Y and N relate to presence and absence, respectively.
ChangeSpeciesTo Taxonomic verification column
CommonNameOther Other common names?
Complete Is this record complete?
AdditionalReferences Additional reference indices.
HostTaxID Host NCBI ID number
HostGenus Host genus
HostFamily Host family
HostOrder Host order
HostClass Host class

pathogen

column name description
PathogenSpecies Pathogen species.
Group Pathogen group (e.g. Protozoa)
AdditionalNotes Some additional notes
PathTaxID Pathogen NCBI ID number
PathGenus Pathogen genus
PathFamily Pathogen family
PathOrder Pathogen order
PathClass Pathogen class
PathKingdom Pathogen kingdom

getNCBI

Function to get taxonomic information for host and parasite species

hostTaxonomy

created with getNCBI, so can be regenerated if/when new data are added.

column name description
HostSpecies original host name from EDWIP
HostTaxID NCBI taxonomic ID
HostGenus Host genus
HostFamily Host family
HostOrder Host order
HostClass Host class

pathTaxonomy

created with getNCBI, so can be regenerated if/when new data are added.

column name description
PathogenSpecies Pathogen species
PathTaxID NCBI taxonomic ID
PathNCBIResolved is the pathogen found in NCBI
PathGenus Pathogen genus
PathFamily Pathogen family
PathOrder Pathogen order
PathClass Pathogen class
PathKingdom Pathogen kingdom

negative

column name description
ERNntr EDWIP record number
PathogenSpecies Pathogen species
DateEntered Date of initial data entry
DateModified Modification date of entry
LogMaxDose Dosage, in many different units
HostStageTested Host stage exposed to pathogen (e.g. Larvae, Nymph, Adult)
HostSpecies Host species examined
Group Pathogen group (e.g. viruses)
HighTaxon General classification of pathogen (e.g. DNA virus)
LowTaxon More specific classification of pathogen (e.g. Baculoviridae)
HostTaxID Host NCBI ID number
HostGenus Host genus
HostFamily Host family
HostOrder Host order
HostClass Host class
PathTaxID Pathogen NCBI ID number
PathGenus Pathogen genus
PathFamily Pathogen family
PathOrder Pathogen order
PathClass Pathogen class
PathKingdom Pathogen kingdom

nemaref

column name description
ERNnem EDWIP record number
refCode Index of reference obtained from nematode data frame
Reference Citation for host-nematode record
HostSpecies Host species
PathogenSpecies Nematode parasite species
HostTaxID Host NCBI ID number
HostGenus Host genus
HostFamily Host family
HostOrder Host order
HostClass Host class
PathTaxID Pathogen NCBI ID number
PathGenus Pathogen genus
PathFamily Pathogen family
PathOrder Pathogen order
PathClass Pathogen class
PathKingdom Pathogen kingdom

nematode

column name description
ERNnem EDWIP record identifier
HostSpecies Host species
PathogenSpecies Nematode parasite species
PathogenStrain Nematode parasite strain
StageInfected Host stage infected
TissueInfected Host tissue infected
FieldOrLab Was this a field or lab tested association?
Country What country did the interaction occur in?
SoilType Type of soil where interaction was observed
AssociatedBacterium Associated bacterium
IntermediateHost Is there an intermediate host present?
CreationDate Date of initial data entry
ModificationDate Modification date of entry
HostTaxID Host NCBI ID number
HostGenus Host genus
HostFamily Host family
HostOrder Host order
HostClass Host class
PathTaxID Pathogen NCBI ID number
PathGenus Pathogen genus
PathFamily Pathogen family
PathOrder Pathogen order
PathClass Pathogen class
PathKingdom Pathogen kingdom

citation

Edgelist of known associations between insect host (Host) and pathogen (Pathogen), and associated references and indexing values. These data are smaller than assocref, which provides more data on host-parasite interactions. CreationDate and ModificationDate are incorrect.

column name description
CitationCode Citation code
Reference Actual citation
CreationDate Record creation date
ModificationDate Record modification date
ReadBy Comments about the reading and identity of reader
GetIt Notes on article acquisition
nvpCount Number of pathogens reported in the citation

We believe assocref are links and citations for nvpassoc, but there are around 3k more rows of data for assocref. However, nvpassoc has more unique host-pathogen association data, so the assocref data may provide multiple citations for the same interaction.

assocref

column name description
ERNnvp EDWIP record number
refCode Reference code
Reference Actual citation
HostSpecies Host species
PathogenSpecies Pathogen species
HostTaxID Host NCBI ID number
HostGenus Host genus
HostFamily Host family
HostOrder Host order
HostClass Host class
PathTaxID Pathogen NCBI ID number
PathGenus Pathogen genus
PathFamily Pathogen family
PathOrder Pathogen order
PathClass Pathogen class
PathKingdom Pathogen kingdom

nvpassoc

column name description
ERNnvp EDWIP record number
PathogenSpecies Pathogen species
Group Pathogen group (e.g. Protozoa)
HostSpecies Host species examined
HostStageTested Host stage exposed to pathogen (e.g. Larvae, Nymph, Adult)
HostTissueInfected Host tissue infected
FieldOrLab Was this a field or lab tested association?
Country What country did the interaction occur in?
IntermediateHost Is there an intermediate host present?
DateEntered Date of initial data entry
DateModified Modification date of entry
BiogeographicRegion Biogeographic region (or some combination thereof)
HostTaxID Host NCBI ID number
HostGenus Host genus
HostFamily Host family
HostOrder Host order
HostClass Host class
PathTaxID Pathogen NCBI ID number
PathGenus Pathogen genus
PathFamily Pathogen family
PathOrder Pathogen order
PathClass Pathogen class
PathKingdom Pathogen kingdom

viraref

column name description
RefCode Index of reference obtained from nematode data frame
Citation Reference
ERNv EDWIP record number
HostSpecies Host species
PathogenSpecies Virus name
HostTaxID Host NCBI ID number
HostGenus Host genus
HostFamily Host family
HostOrder Host order
HostClass Host class
PathTaxID Pathogen NCBI ID number
PathGenus Pathogen genus
PathFamily Pathogen family
PathOrder Pathogen order
PathClass Pathogen class
PathKingdom Pathogen kingdom

viruses

column name description
ERNv EDWIP record number
HostSpecies Host species
VirusType DNA or RNA virus
PathogenSpecies Viral family
Virus Virus identity
HostStageInfected Host stage infected
HostTissueInfected Host tissue infected
FieldOrLab Was this a field or lab tested association?
Country What country did the interaction occur in?
IntermediateHost Is there an intermediate host present?
CreationDate Date of initial data entry (wrong)
ModificationDate Modification date of entry (wrong)
ProvinceA Canadian provinces where host-virus interaction occurs
PathogenValue Is there value to the pathogen (can it be used as a control agent?)
Group Viruses
HostTaxID Host NCBI ID number
HostGenus Host genus
HostFamily Host family
HostOrder Host order
HostClass Host class
PathTaxID Pathogen NCBI ID number
PathGenus Pathogen genus
PathFamily Pathogen family
PathOrder Pathogen order
PathClass Pathogen class
PathKingdom Pathogen kingdom

noassref

These data are included because they were originally part of the EDWIP data. We caution the user in using these data, as they do not have associated metadata that the other records have.

column name description
RefCode Index of reference
ERNntr EDWIP record number
HostSpecies Host species
PathogenSpecies Virus name
Citation Citation for host-pathogen record
HostTaxID Host NCBI ID number
HostGenus Host genus
HostFamily Host family
HostOrder Host order
HostClass Host class
PathTaxID Pathogen NCBI ID number
PathGenus Pathogen genus
PathFamily Pathogen family
PathOrder Pathogen order
PathClass Pathogen class
PathKingdom Pathogen kingdom

new_asso

These data are included because they were originally part of the EDWIP data. We caution the user to not use these data, as we do not believe the records are correct.

column name description
ERNnew EDWIP record number
HostSpecies Host species
HostOrder Host order
HostFamily Host family
HostHabitat Habitat type of host
HostFood What does the host eat?
HostGenYr Number of generations of hosts per year
PathSpecies Nematode species
PathGroup Pathogen group (fungi, protozoa, nematode, etc.)
PathHighTaxon Pathogen taxonomic information (mostly NA)
PathLowTaxon Pathogen taxonomic information (mostly NA)
StageInf Host life stage infected
TissueInfected Host tissue infected
Field Was this a field or lab tested association?
Country Country of host-pathogen association
IntermediateHost Information on intermediate hosts
Citation Citation for host-pathogen record
MoreInfo Additional comments or notes
Who Identity of researcher who entered data
CreationDate Record creation date
ModificationDate Record modification date
StainFCB takes values: Adult, egg, larvae, pupa

newnema

These data are identical to the nematode data, as far as we can tell.

column name description
ERNnem EDWIP record identifier
Host Host species
Nematode Nematode parasite species
NemaOrder Pathogen order
NemaFamily Pathogen family
NemaStrain Pathogen strain
StageInfected Host stage infected
TissueInfected Host tissue infected
FieldOrLab Was this a field or lab tested association?
Country What country did the interaction occur in?
SoilType Type of soil where interaction was observed
AssociatedBacterium Associated bacterium
IntermediateHost Is there an intermediate host present?
CreationDate Date of initial data entry
ModificationDate Modification date of entry
Group all just say 'nematode'

Install

Install from GitHub using the code below.


# install.packages("devtools")
devtools::install_github("viralemergence/insectDisease")
library("insectDisease")

vignette

The raw data can be called using the data() function on the various files within the R folder. In the vignette folder, there is some code that cleans, processes, and taxononymizes the data.

When using this database, cite this reference

Braxton, S. M., et al. "Description and analysis of two internet-based databases of insect pathogens: EDWIP and VIDIL." Journal of Invertebrate Pathology 83.3 (2003): 185-195.

Also, this database was originally created by the following people, to whom we are indebted:

  • David W. Onstad, EDWIP Director. Center for Economic Entomology, Illinois Natural History Survey

  • Ellen Brewer, Research Programmer. Center for Economic Entomology, Illinois Natural History Survey

  • Susan Braxton, Science & Technology Librarian. Milner Library, Illinois State University

Contribute!

Feel free to fork it and contribute some functionality.

Funding

This work has been supported by funding to the Viral Emergence Research Initiative (VERENA) consortium, including a grant from the U.S. National Science Foundation (NSF-BII-2021909) and a grant from Institut de Valorisation des Données (IVADO).

This study is supported by the U.S. National Science Foundation Research Coordination Network (NSF/NIH/USDA DEB 131223).


Meta

  • Please report any issues or bugs.
  • License: GPL-3
  • Get citation information for insectDisease in R doing citation(package = 'insectDisease')
  • Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

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An R package for working with the Ecological Database of the World's Insect Pathogens (EDWIP)

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