USGS NWHC - Laboratory Information Management System - US - Avian Pox and Poxviruses

Latest version published by United States Geological Survey on Aug 31, 2016 United States Geological Survey
Publication date:
31 August 2016
CC0 1.0

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The LIMS (laboratory information management system) database is a computerized record of specimens - from serum samples to carcasses - sent to the National Wildlife Health Center (NWHC) for processing and diagnostic workup. Data include history and recordkeeping information (identifier numbers, species, sex, submitter information, etc); types of tests run (virology, bacteriology, parasitology, chemistry, etc.) and some test results for heavy metals, particularly lead; and diagnostic results. The diagnostic coding system is based on SNOMED terminology, with certain modifications and additions to fit Center needs. SNOMED, the Systematized Nomenclature of Medicine, is a structured nomenclature and classification of the terminology used in human and veterinary medicine. Terms are assigned in any or all of the following six categories for each diagnosis: topography - detailed anatomic term for the site of interest; morphology - information on the pathogenic change or process associated with the topography; etiology - cause or causal agent of the disease or dysfunction; disease - disease, disease entity or syndrome; link - qualifier to link one diagnosis to another. These data include occurrence records for Avian Pox and poxviruses for the entire US, by the USGS National Wildlife Health Center (NWHC).


The table below shows only published versions of the resource that are publicly accessible.

How to cite

Researchers should cite this work as follows:

Cleary, K.R. 1995. Diagnostic Database Coding Dictionary. National Wildlife Health Center, Madison, WI. 66 pp.


Researchers should respect the following rights statement:

The publisher and rights holder of this work is United States Geological Survey. To the extent possible under law, the publisher has waived all rights to these data and has dedicated them to the Public Domain (CC0 1.0). Users may copy, modify, distribute and use the work, including for commercial purposes, without restriction.

GBIF Registration

This resource has not been registered with GBIF


Metadata; occurrence; observation; wildlife; epizootics; mortality; morbidity; disease; avian; mammal; endangered species; bird; wildlife health; amphibian; reptile; marine invertebrate; endangered species; virus; pathogen; vector; host; Metadata

External data

The resource data is also available in other formats

USGS WDHC Quarterly Mortality Reports UTF-8 Adobe pdf


Karen Cunningham
  • Custodian Steward
  • Originator
Data Manager
National Wildlife Health Center
6006 Schroeder Road
53711-6223 Madison
Annie Simpson
  • Metadata Provider
biologist and information scientist
USGS Core Science Analytics Synthesis and Libraries Program
12201 Sunrise Valley Drive, Mailstop 302
20192 Reston
+1 703-648-4281
Jennifer Buckner
  • Point Of Contact
  • Principal Investigator
Diagnostic Database Manager
National Wildlife Health Center
6006 Schroeder Road
53711-6223 Madison
David Blehert
  • Point Of Contact
Branch Chief, Disease Investigations
National Wildlife Health Center
6006 Schroeder Road
53711-6223 Madison

Geographic Coverage

US and Territories, including Midway Island and Puerto Rico.

Bounding Coordinates South West [17.61, -178.93], North East [71.48, -66.29]

Taxonomic Coverage

Avian Pox and host organisms.

Class Aves (Birds)
Genus Avipox Virus (Avian Pox)

Temporal Coverage

Start Date / End Date 1980-01-01 / 2014-01-01

Project Data

No Description available

Title USGS - Wildlife Health Diagnostic Database, Laboratory Information Management System (LIMS), entire US, Avian Pox and Poxviruses
Funding Unites States Geological Survey Ecosystems Mission Area
Study Area Description LIMS is a process-based record of samples sent to NWHC, and includes documentation on how samples and data move through the Center, as well as results information sent back to the submitter and other contacts. It may not be a representative sample of mortality for any particular species or group; however, the database can be used to determine if a disease/syndrome existed. For example, the database can be used to document avian cholera in mallards in California at a particular location or time, but it cannot be used to say that there was more cholera in 1990 than in 1980, since the number of specimens submitted for diagnostic workup does not necessarily reflect the total number of mortalities. Individuals interested in documenting total mortalities should reference the Epizootiological Database (EPIZOO), also maintained at NWHC.
Design Description The datafile was developed and is maintained by personnel at NWHC and is the result of years of diagnostic work by Center personnel. However, federal, state, tribal, and local agencies, universities and private individuals have all been involved as contributors to the system and their assistance should not be ignored.

The personnel involved in the project:

Leanne White
  • Custodian Steward

Sampling Methods

A complete description of the data set is provided in the document referenced in 5.2.2 (Diagnostic Database Coding Dictionary), including field lengths, descriptions and attribute value indicators.

Study Extent Federal, state, tribal and local agencies, universities, private individuals and foreign governments have all been involved as contributors to the system; all have submitted samples and/or carcasses for diagnostic evaluation and have provided the history portion of the database.
Quality Control Data are verified upon completion by case pathologist. Random subsets of records are verified for all fields on an intermittent basis. Values for selected fields are constrained and tested during data entry. When all work is complete, an assigned pathologist/clinician is responsible for reviewing the information, verifying its accuracy, determining a final diagnosis and issuing a final report. A summary of this information is then incorporated into the master file and becomes a part of the permanent record.

Method step description:

  1. Various NWHC standard operating procedures are utilized during data processing - interested individuals should reference the NWHC SOP manual for specifics. Contact the PROCESS CONTACT listed below for additional information.

Bibliographic Citations

  1. USGS National Wildlife Health Center. Resources on Avian Pox and Poxviruses. Accessed 2015-07-20.

Additional Metadata