| Title: | Ecological Database of the World's Insect Pathogens |
|---|---|
| Description: | David Onstad provided us with this insect disease database, sometimes referred to as the 'Ecological Database of the Worlds Insect Pathogens' or EDWIP. Files have been converted from 'SQL' to csv, and ported into 'R' for easy exploration and analysis. Thanks to the Macroecology of Infectious Disease Research Coordination Network (RCN) for funding and support. Data are also served online in a static format at <https://edwip.ecology.uga.edu/>. |
| Authors: | Tad Dallas [aut, cre] |
| Maintainer: | Tad Dallas <[email protected]> |
| License: | GPL-3 |
| Version: | 1.2.3 |
| Built: | 2025-02-15 06:28:04 UTC |
| Source: | https://github.com/viralemergence/insectDisease |
Edgelist of known associations between insect host ('Host') and pathogen ('Pathogen'), and associated reference and indexing values. The variables are as follows:
data(assocref)data(assocref)
A data.frame with 11005 observations
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
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. The variables are as follows:
data(citation)data(citation)
A data.frame with 1966 observations
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.
Process through a vector of species names to obtain taxonomic data
getNCBI(species, host = TRUE)getNCBI(species, host = TRUE)
species |
a vector of species names |
host |
(boolean) affects column naming (nice to keep host and pathogen separate) |
a data.frame with nrow == length(species)
## Not run: mouse <- getNCBI("Peromyscus leucopus") worm <- getNCBI("Ascaris lumbricoides", host=FALSE) ## End(Not run)## Not run: mouse <- getNCBI("Peromyscus leucopus") worm <- getNCBI("Ascaris lumbricoides", host=FALSE) ## End(Not run)
Data on host species taxonomy, habitat, diet preferences, and distribution (in Canada)
data(hosts)data(hosts)
A data.frame with 4392 observations
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. Can be <1, =1, >1, or some combination of these.
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
Host taxonomic cached data from NCBI (see vignette for code to re-make)
HostSpecies original host name from EDWIP
HostTaxID NCBI taxonomic ID
HostGenus host genus
HostFamily host family
HostOrder host order
HostClass host class
data(hostTaxonomy)data(hostTaxonomy)
A data.frame
This package provides a 'R' workspace with insect disease database data already present. Data are visible by using the R command ls("package:InsectDisease")', and individual data frames can be imported to your local workspace by using the command 'data(NAMEOFDATA)'
Data frames can be grouped by parasite type, as 'nemaref', 'nematode' and 'newnema' provide information on nematode infections, as 'nvpassoc' provides information on protozoans, and 'viraref' and 'viruses' provide details of viral infections. 'pathogen' provides general taxonomic information on pathogens in the database. Citations are available in a number of places, including but not limited to 'assocref', 'citation', 'nemaref', and 'viraref'.
*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
Maintainer: Tad Dallas [email protected]
Useful links:
Report bugs at https://github.com/viralemergence/insectDisease/issues/
Hosts were challenged with pathogen, and did not become infected. These are data on what pathogens do not infect certain hosts.
data(negative)data(negative)
A data.frame with 529 observations
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
Edgelist of known associations between insect host ('Host') and nematode parasite ('Nematode'), and associated references and indexing values. These data are smaller than 'assocref', and 'citation'. The variables are as follows:
data(nemaref)data(nemaref)
A data.frame with 338 observations
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
Host associations for nematode parasites
data(nematode)data(nematode)
A data.frame with 234 observations
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
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.
These data are included because they were originally part of the EDWIP data. These data are identical to the 'nematode' data, as far as we can tell.
data(new_asso) data(newnema)data(new_asso) data(newnema)
A data.frame of not good records
A data.frame
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
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'
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.
data(noassref)data(noassref)
A data.frame
RefCode. Index of reference
ERNntr. EDWIP record number
HostSpecies. Host species
PathogenSpecies. Pathogen species
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
Non-viral parasite (protozoan, fungi, bacteria) occurrences on host species. The variables are as follows:
data(nvpassoc)data(nvpassoc)
A data.frame with 7164 observations
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
Information on taxonomy of parasites present in this database
data(pathogen)data(pathogen)
A data.frame with 2041 observations
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
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
data(pathTaxonomy)data(pathTaxonomy)
A data.frame
Edgelist of known associations between insect host ('Host') and viral pathogen ('Virus'), and associated references and indexing values. These data are smaller than 'assocref', and 'citation'. The variables are as follows:
data(viraref)data(viraref)
A data.frame with 2124 observations
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
Host associations for viruses
data(viruses)data(viruses)
A data.frame with 1659 observations
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