Data to EDWIP
Species names for hosts and pathogens (except viruses) consist of a genus, specific epithet, and possibly a subspecies. All terms occur together in one field, with a single space between terms. Author names are not included in EDWIP for any organism group. Scientific names are not italicized or underlined. This method is followed for hosts, bacteria (including symbiont bacteria associated with nematodes), fungi, mollicutes, protozoa, and nematodes. Viruses are handled differently; see section on viruses.
Every attempt is made to determine the current, correct name of hosts and pathogens. In this effort, we have had help from authorities on all groups of organisms (see Acknowledgments page).
Synonyms and common misspellings of host species are included in EDWIP. These do not represent an exhaustive nomenclatural history for host species. They are restricted to alternate names (synonyms and common misspellings) which we have encountered, primarily in the pathology literature. They are intended to provide reasonable access to the pathogen association records by host names familiar to users, and do not represent an exhaustive nomenclatural history for host species. Alternate host names are entered as genus, species, and subspecies (if applicable). Multiple synonyms or misspellings are separated by commas within the synonym field.
Synonyms of pathogen species are not searchable in EDWIP.
Taxonomy and Classification
Species names are entered as outlined above in the Scientific Names section.
We make every attempt to verify scientific names of hosts using appropriate catalogs for the groups in question. See our Auxiliary References page for a list of catalogs we have used. We use family and order names from Common Names of Insects and Related Organisms, 1997, Joseph J. Bosik, chairman, Committee on Common Names of Insects, Entomological Society of America, wherever possible.
The number of generations per year is either =1, <1, >1. If different populations have different numbers of generations per year, a combination of these may be entered.
Host habitat(s) are entered into a single text field, in no particular order. Several habitats may be entered for a host species. When different life stages of hosts occupy different habitats, life stages may be indicated with the habitat (e.g., larvae: aquatic). Additional terms may be used to further describe or qualify the habitat (e.g., open woodland, forest edges, dry grassland). An index of host habitats used in EDWIP is given on the Indexes page.
Foods of host organisms may be entered as either scientific or vernacular names. We try to include the scientific names wherever possible. For polyphagous hosts, food may be summarized in groups (e.g., "most deciduous trees", "all Solanaceae"). Food(s) are entered as a text string, in no particular order, into a single field. Information about host food(s) may come from the reference describing the pathogen association, but most often comes from a separate reference (see our list of Auxiliary References). An index of food terms used in EDWIP is given on the Indexes page.
Diabrotica undecimpuncata howardii
Balsam fir (Abies balsamea), alpine fir (Abies lasiocarpa), tamarack (Larix laricina), white spruce (Picea glauca), black spruce (Picea mariana), red spruce (Picea rubins), Englemann spruce (Picea engelmannii), various pines (Pinus spp.)
Greenbeans, soybeans, can be found on more than 200 of the common weeds, grasses and cultivated crops.
Species names are entered as outlined above in the Scientific Names section.
Pathogen species are assigned to pathogen groups and then to high taxa and low taxa within those groups. The actual level of classification represented by the high and low taxa vary across pathogen groups, and are based on conventions used for those groups by pathologists.
Names and classifications for viruses and nematodes are not entered into the Pathogen Classification file, due to separate treatment of these groups in EDWIP. However, they do have high and low taxon designations.
High and low taxa and other specific protocols for each pathogen group are listed by pathogen group.
Bacteria | Fungi | Mollicutes | Protozoa | Nematodes | VirusesBacteria
High taxa are actinomycetes, spore-forming bacteria, and non-spore-forming bacteria.
Low taxa are the families mentioned in Tanada and Kaya 1993.
The Bacilliaceae are the spore-forming bacteria.
High taxa are classes.
Low taxa are orders with "unknown" entered for all fungi imperfecti.
Both high and low taxa are based on Alexopoulos et al. (1996) because coverage is more complete than in Tanada and Kaya (Table 10-1).
Deuteromycetes is used for all fungi imperfecti.
Fungal varieties are included as part of the species field, if given.
Coelomomyces iliensis var. indus
High taxa are Mycoplasma and Spiroplasma.
Low taxa are the families Mycoplasmataceae and Spiroplasmataceae.
High taxa are phyla, according to Tanada and Kaya 1993 (Table 11-1).
Low taxa are orders, according to Tanada and Kaya 1993 (Table 11-1).
The Class Coccidia has been included (in the High Taxon field) with its single order Adeleida to permit searching for this well-known term.
Orders for the Zoomastigina and for Ciliophora, Class Litostomatea are not listed in Tanada and Kaya (1993). We have used Kinetoplastida for the one order of Zoomastigina species.
Two orders of Apicomplexa not listed by Tanada and Kaya 1993 are used: Haemospororida and Piroplasmorida.
Because many nematologists requested that nematode strain, soil type, bacterial symbiont, be included, a separate nematode file was created to accommodate these data requirements.
High taxa are orders.
Low taxa are families.
Strain is entered when that information is available. If the strain is listed as "not maintained", this is entered in the strain field.
The soil type and habitat from which the association was observed are entered when this information is available. Some soil type examples are: clay; clay loam; loam; sandy loam; loamy sand; sand. Habitats follow terms given under Host Ecological Data, above.
Bacterial symbionts of nematode species are entered, but not linked to the pathogen file. (NOTE: Photorhabdus is the correct genus for bacteria associated with Heterorhabditis species, not Xenorhabdus luminescens, Boemare et al. 1993).
If a record is based on a report of a species of virus, the complete name of the insect species is entered as a prefix in front of the virus or virus acronym. The host species prefix is included if authors use one, or if the virus was isolated from a field specimen of host.
If a record is based on a report of a disease in a host (as opposed to a virus species), no host species prefix is included.
The following acronyms taken from Tanada and Kaya (1993) are used for the virus species:
- AV ascovirus
- CPV cytoplasmic polyhedrosis virus
- DNV densonucleosis virus
- EPV entomopoxvirus
- GV granulosis virus
- IV iridescent virus
- NOB non-occluded baculovirus
- NPV nuclear polyhedrosis virus
Other virus names are written out. The acronym PV is not used, because many viral family names start with the letter P.
Polydnaviruses are not included in EDWIP.
Virus-like diseases are entered only when the family is known.
High taxa are the viral types RNA or DNA.
Low taxa are families according to Tanada and Kaya (1993, Figures 6-2 and 8-1).
Type of Record
Cydia pomonella GV
The protocol applies to all associations, whether in the Nonviral Pathogen Association file, the Nematode Association file, or the Virus Association file.
Number of Species per Record
One species of primary host and one species of pathogen are entered per record. An intermediate host species may be entered, if reported. For nematodes, the associated bacterial symbiont species may be entered, if it is known.
Undescribed or Unidentified Species
If the genus is known, undescribed or unidentified species may entered into EDWIP. The rules for including or excluding association entries when only the genus of host and/or pathogen is known are as follows:
- Genera unique to the database are entered (i.e., EDWIP contains no records for the genus).
- Pathogen genera are entered if the association of that genus with the host species is unique in EDWIP (e.g., because a record of Nosema pyrausta infecting Ostrinia nubilalis is already in EDWIP, an unidentified Nosema sp. infecting O. nubilalis would not be entered.)
- The host genus is entered if the association of that genus with the pathogen species is unique in EDWIP.
- A published comparison of described and undescribed pathogen species may lead to the entry of the genus in some cases.
Host Stage Infected
All major life stages (i.e., Egg, Numph, Larva, Pupa, Adult, or a combination of these) of the host reported to be infected by the pathogen are entered. We do not distinguish among larval and nymphal instars.
Host Tissues Infected
The tissue(s) infected are entered as a text string into a single field. In general, we enter little detail, but we do follow terminology used in the references supporting the association. We may specify tissues infected by life stage or sex of host (e.g., Adipose tissue of larvae; oenocytes, ovary of adult females.) An index of tissues is given on the Indexes page.
A host species that is required, in addition to the named primary host, to complete the pathogen life cycle is an intermediate host. For most pathogens, intermediate hosts either do not exist or are unknown, and the field is left blank. If the intermediate host is an insect or insect ally, a separate record will also list it as the primary host.
The location of the observed association is entered as "field" or "lab" or "information not available." If the association was observed in a specimen collected anywhere outside of a laboratory colony, "field" is entered. Greenhouse observations are considered field observations. If any report of the association qualifies as a "field" observation, "field" will be the only location reported in EDWIP. The distinction between lab and field associations is made to distinguish those associations that may be considered to occur naturally somewhere in the world from those that have been observed in the lab only. NOTE: The association may not occur naturally in all countries listed in the Country of Observation field.
Country of Observation
One or more countries of observation may be listed. USA (without periods) is used for United States of America. Island names may be appended to country names to distinguish them from mainland observations (e.g., USA-Hawaii). Country names are entered as reported in the citations supporting the associations, and are not updated to reflect current geopolitical conditions. A index of country names used in EDWIP is given on the Indexes page.
Citations supporting associations are entered with the associations. Because EDWIP is not intended to be a comprehensive bibliographic database, our standard practice has been to enter up to 5 citations per association record. Additional citations may be added to support an association when they represent an original report of research on an association, or when they include information new to EDWIP (i.e., a new host stage or tissue, or a new locality). In general, we do not strive to present an exhaustive bibliography on each association, but rather to provide access to some published reports of the association.
Negative Test Results
Number of Species per Record
One species of host and one species of pathogen are entered per record.
All major life stages (i.e., Egg, Nymph, Larva, Pupa, Adult, or a combination of these) of the host tested and not infected are entered. We do not distinguish among larval and nymphal instars. If one stage can be infected and another cannot (excluding separate larval or nymphal stages), then an association record may be entered as well as a negative test result record. If some larval or nymphal instars are infected but others are not, then no negative test result record is entered, and the pathogen is reported as infecting the nymph or larva in the appropriate association file.
Logarithm of Maximum Dose
For the logarithm of maximum dose, we entered a whole number from 1 to 10, with 1 representing 10 to the first power or 10 units and 9 representing 10 to the ninth power or 1 billion units. We included the volume or area in which the units are applied such as ml, cm2, or ha. Exponents are not used. Only the maximum dose tested is entered. For example, 4 pibs/ml means 10,000 pibs/ml.
Citations in this file are limited to those which support records in the three association files (Nonviral Pathogen, Nematode, Virus) and the Negative Test Results file. Those references used to clarify or verify scientific names and classifications of hosts and pathogens, or to gather ecological data on hosts are maintained as an Auxiliary References list only, and are not part of EDWIP's database structure.
Reference codes are sequential, automatically assigned numbers. Codes are used to link citations to the association files (Nonviral Pathogen, Nematode, and Virus) and the Negative Test Results file.
Citations are entered in a single text field, as one string consisting of the author(s), year, title, and source (for articles, chapters, or conference papers), or author(s), title, publisher, year (for books). No special formatting (underlines, italics, indenting, etc.) is used.
All authors are listed with last name first, followed by initials. Multiple authors are separated by commas or semicolons.
Journal titles may be entered as full titles or in abbreviated form in our citation records. Abbreviations of journal titles are not standardized (but we are working towards eliminating abbreviations).
The language of publication, if not English, is generally indicated.
David W. Onstad (firstname.lastname@example.org)
This page last updated May 31, 2001 -- SMB