USGS NWHC - Laboratory Information Management System - Eastern US - Avian Cholera and Pasteurella multocida

Karen Cunningham1, Annie Simpson2, Jennifer Buckner1, David Blehert1

1 National Wildlife Health Center, 6006 Schroeder Road, 53711-6223, Madison, United States; 2 US Geological Survey Core Science Analytics Synthesis and Libraries Program, 12201 Sunrise Valley Drive, Mailstop 302, 20192, Reston, United States

Corresponding author(s): Karen Cunningham (kcunningham@usgs.gov), Annie Simpson (asimpson@usgs.gov)

Received {date}; Revised {date}; Accepted {date}; Published {date}

Citation: Combination of authors, year of data paper publication (in parentheses), Title, Journal Name, Volume, Issue number (in parentheses), and doi of the data paper.

Resource Citation

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

Abstract

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 Cholera and hosts for eastern US, by the USGS National Wildlife Health Center (NWHC).

Keywords: 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

Project details

Project title: USGS - Wildlife Health Diagnostic Database, Laboratory Information Management System (LIMS), Eastern US, Avian Cholera and Pasteurella multocida
Personnel: Leanne White
Funding: Unites States Geological Survey Ecosystems Mission Area
Study area descriptions/descriptor: 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.

Data published through GBIF: https://bison.usgs.gov/ipt/resource?r=usgs-nwhc-easternus-limsaviancholera

Taxonomic coverage

General taxonomic coverage description: Pasteurella multocida (Avian Cholera) and its host organisms (birds).
Taxonomic ranks
Class: Aves
Species: Pasteurella multocida
Common names: Avian Cholera, birds

Spatial coverage

General spatial coverage: Eastern United States.
Coordinates: 24°43'12''N and 49°1'12''N Latitude; 93°40'12''W and 66°38'24''W Longitude 

Temporal coverage: 1975 - 2014

Methods

Method step description: 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.
Study extent description: 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.
Sampling description: 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.
Quality control description: 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.

Datasets

Dataset description
There is no dataset published through Darwin Core Archive format for this resource. Currently described datasets are listed in the section External datasets.
Language: English
Licences of use: To the extent possible under law, the publisher has waived all rights to these data and has dedicated them to the <a href="http://creativecommons.org/publicdomain/zero/1.0/legalcode">Public Domain (CC0 1.0)</a>. Users may copy, modify, distribute and use the work, including for commercial purposes, without restriction.

External datasets

Dataset description
Object name: USGS WDHC Quarterly Mortality Reports
Character encoding: UTF-8
Format name: Adobe pdf
Distribution: http://www.nwhc.usgs.gov/publications/quarterly_reports/index.jsp

Metadata language: English
Date of metadata creation: 2015-07-17
Hierarchy level: Dataset

References
USGS National Wildlife Health Center. Information on Avian Cholera, Pasteurella multocida. Accessed 2015-07-20. http://www.nwhc.usgs.gov/disease_information/avian_cholera/