Introduction to Protocol Manager

1
Introduction to Protocol Manager Lanie Paquin,
USBR PN-Region GIS June 20, 2006
2
I. Introduction

• What is Protocol Manager?
• Relational database application
• Dynamic data dictionary
• Data management tool

3
I. Introduction

• B. What does Protocol Manager do?
• Supports biological monitoring programs and
  projects
• Fully documents data elements and their
  properties
• Cites method reference documents

4
I. Introduction

• C. Who is interested in Protocol Manager?
• U.S. Bureau of Reclamation Spatial Dynamics
• National Park Service USFS (Fire Ecology)
• NOAA Fisheries Northwest Fisheries Science Center
  (NWFSC)
• USGS National Biological Information
  Infrastructure (NBII)
• NED PNAMP Effectiveness Monitoring Group
• State of Washington
• Wenatchee Sub-basin RTT
• Streamnet

5
I. Introduction

• D. Why use Protocol Manager?
• Foster coordination and collaboration
• Improve data quality consistency
• Enforce data standards
• Provide data transparency
• Facilitate data exchange and usage
• Compare, improve, and develop protocols

6
I. Introduction

• E. Whats next for Protocol Manager?
• 1. Support Pacific Northwest Aquatics
  Monitoring Partnership (PNAMP) Workgroup
  functions
• Data analysis
• Content management
• Protocol standards

7
I. Introduction

• E. Whats next for Protocol Manager?
• 2. Partner with National Resource Monitoring
  Partnership (USGS NBII, et al.) Protocol Library
  and Monitoring Locator National Project
• Form regional consortium node
• Leverage NBII Information Technology (IT)
  resources
• Utilize national and international scientific
  expertise

8
II. RME Data Management Pilot Overview

• Brief History
• FCRPS 2000 BiOp - Research, Monitoring
  Evaluation (RME) - Data Management Work Plan, May
  2003
• John Day Pilot, October 2003
• Data Analyst
• Data Dictionary

9
II. Pilot Overview

• Brief History
• 3. Coordinate with Wenatchee Regional Technical
  Team (RTT) Pilot
• a. Upper Columbia Monitoring Strategy, Hillman,
  February 2004
• 4. Publish John Day ( U.Columbia) Data
  Dictionary, June 2004

10
II. Pilot Overview

• Brief History
• 5. Effectiveness monitoring host database design
  process, June 2004
• a. ArcHydro geospatial data model concepts and
  relationships applied to monitoring data
• b. NPS (Fire Ecology Assessment Tool) FEAT
  Protocol Manager DB (.vba) application replaces
  static data dictionary

11
II. Pilot Overview

• Brief History
• 6. NOAAF NWFSC Status Trend Monitoring (STM)
  Database initiated, September 2004
• a. Wenatchee 2004 physical and biological data
  loading completed, August 2005
• b. EMAP (ODEQ Wenatchee) PIBO 2004 loading
  in progress at NWFSC

12
II. Pilot Overview

• Brief History
• 7. National Resource Monitoring Partnership
  Protocol Library and Monitoring Locator Project
  initiated, November 2005.
• USGS NBII, National Park Service (NPS),
  International Association of Fish and Wildlife
  Agencies (IAFWA)
• USGS NBII 500K Technical Resources

13
II. Pilot Overview

• Brief History
• 8. Current Status
• Version 0.7x (.Net)
• June 2006 release
• NPS National Interagency Fire Center (NIFC) (Nate
  Benson, et al.) cost share through contractor
• Protocol Manager User Documentation due August
  2006
• Desktop Installations
• Multiple versions of database contents require
  coordination

14
II. Pilot Overview

• Brief History
• 8. Current Status
• c. U.S. Government owns software code (public)

15
II. Pilot Overview

• Brief History
• 9. Next Steps
• Grow Protocol Manager Project Partnership
• NED/PNAMP
• NRMP/USGS NBII
• Develop Version 2.0
• Fully Functional Suite of Features
• Plan Web Enabled Application
• Centralized Relational Database Management System
  Host Services Oriented Architecture

16
II. Pilot Overview
B. Key RME Data Management Pilot Findings 1.
Protocols are integral to monitoring data a.
Protocols Metadata b. Metadata Data c.
Protocols Data
17
II. Pilot Overview
B. Key RME Data Management Pilot Findings 2.
Protocols are defined by their data management
functions a. Prescribe data elements b.
Describe methods and procedures i. Collect
field data ii. Process summary values iii.
Validate values
18
II. Pilot Overview
B. Key RME Data Management Pilot Findings 3.
Data management systems must be designed from an
end-to-end perspective (from data collection
through data entry to database management, report
generation and data sharing). Data Management
for Field Collection, June 2004, Welches, OR Data
Management Workshop
19
III. Monitoring Data Processes
A. Analytical Framework Empirical Method
20
III. Monitoring Data Processes
B. Field Data Processing Flow
Subject Matter Expert
Data Analyst
Data Steward
Prep for field
Record data
Update repository
Analyze indicators
Collect data
Capture data
Transfer data
Field Worker
Researcher
Coordinator
21
III. Monitoring Data Processes
C. Interaction between Tabular Data and ArcHydro
Geodatabase
Raw Data
Foreign Keys
Generated Data
ArcHydro
Protocols
Analysis
Feature ID
22
Protocol Manager
Monitoring Program
Revise Protocols/ Methods
Document Protocols/ Methods
Evaluate Protocols/ Methods
Protocol
Data Collection Methods
Data Validation Methods
Data Summary Methods
Data Analysis
Status Trend Monitoring Database
Field Forms
Repository Database
Field Data Tables
23
IV. Protocol Manager Concepts

• Monitoring Programs Protocols
• Terms
• Relationships of Terms
• Protocol Manager
• Comparing Protocols Methods

24
Monitoring Programs Protocols
Monitoring Program Protocols Specified
EMAP
EMAP (2001)
PNAMP
(w/ OWEB for Bank Stability)
EMAP (2001)
PIBO
PIBO (2002)
PIBO (2004)
PIBO (2003)
John Day AFG
EMAP (2001)
PIBO (02-04)
plus other protocols in development or
undocumented
Upper Columbia Monitoring Strategy
EMAP (2001)
OPSW (1999)
WFC (1998)
WDFW (2000)
WFPB (1983)
Zaroban (2000)
Schuett-Hames (1999)
BURPTAC (1999)
Hawkins et al. (1993)
Overton et al. (2000)
Platts et al. (1983)
Parmenter et al. (2003)
Strange (1996)
Dolloff et al. (1996)
Reynolds et al. (1996)
Reeves et al. (2001)
Van Deventer and Platts (1989)
Borgerson et al. (1992)
Anderson and Neumann (1996)
Mosey and Murphy (1996)
and more
25
Terms
Subject Area
Indicator
Indicator Group
Escapement/number Age structure Size Sex
ratio Origin (hatchery or wild) Genetics Fecundity
Biological
Adults
Protocol
Method
Attribute
Redds
Number Distribution
Abundance/distribution Size parr
Parr / Juveniles
Number smolts Size smolts Genetics smolts
Smolts
Transport Composition
Macro invertebrates
26
Relationships of Terms
Protocol
Collection Method
Indicator
Attribute Name
Attribute Name
Indicator Group
Attribute Name
Indicator
Summary Method
Summary Value
Indicator
Collection Method
Attribute Name
27
Relationship of Terms
EMAP, 2001
Dominate Substrate
Dominant Substrate (EMAP, 2001)
Fields from data collections
Distance Left Bank
DIST_LB
Bankfull Depth
BF_DEPTH
Size Class Code
SIZE_CLS
Embeddedness
EMBED
Substrate Flag
FLAG_SUB
Transect
TRANSECT
Collection Attributes
Transect Position
TRANSDIR
Comments
COMMENTS
Habitat Event ID
HAB_EVENT
Links to Site info Site ID, Date, Stream ID,
Visit No., Team ID, Location, etc.
Large Wood Debris
28
Protocol Manager
Protocol
Short Name EMAP, 2003
Name EMAP West Surface Water Wadeable Streams
Contact Phil Kaufman
Doc Ref Peck, et al., 2003, EMAP West Surface
Water Wadeable Streams, EPA,
Corvallis,OR
-
Library Protocols
-
EMAP Surface Waters Wadeable Streams, 2003
Bank Measurements
Large Woody Debris

Bank Measurements
Procedure
Procedure

Large Woody Debris
Attribute
Attribute
Torrent Evidence

Procedure
Procedure
Attribute
Attribute

Stream Flow - NBO
Procedure
Procedure
Attribute
Attribute
Procedure
Procedure
Attribute
Attribute
Methods
Torrent Evidence
Stream Flow - NBO
Procedure
Procedure
Attribute
Attribute
Procedure
Procedure
Attribute
Attribute
Procedure
Procedure
Attribute
Attribute
Procedure
Procedure
Attribute
Attribute
29
Comparing Protocols Methods
Large Woody Debris
EMAP, 2001
Merritt, 2004
Large Woody Debris (EMAP, 2001)
Field Name
Attribute Name
Large Woody Debris (Merritt, 2004)
Bankfull Diameter 0.1-0.3m Length 1.5-5m
WETSDSL
Field Name
Attribute Name
Bankfull Diameter 0.3-0.6cm Length 1.5-5m
WETMDSL
Bankfull Diameter 0.6-0.8m Length 1.5-5m
WETLDSL
Bankfull Diameter 10-15cm Length 1-3m
10_SHT
Bankfull Diameter gt0.8m Length 1.5-5m
WETXDSL
Bankfull Diameter 10-15cm Length gt3-6m
10_MED
Bankfull Diameter 0.1-0.3m Length 5-15m
WETSDML
Bankfull Diameter 10-15cm Length gt6m
10_LON
Bankfull Diameter 0.3-0.6cm Length 5-15m
WETMDML
Bankfull Diameter gt15-30cm Length 1-3m
15_SHT
Bankfull Diameter 0.6-0.8m Length 5-15m
WETLDML
Bankfull Diameter gt15-30cm Length gt3-6m
15_MED
Bankfull Diameter gt0.8m Length 5-15m
WETXDML
Bankfull Diameter gt15-30cm Length gt6m
15_LON
Bankfull Diameter 0.1-0.3m Length gt15m
WETSDLL
Bankfull Diameter gt30cm Length 1-3m
30_SHT
Bankfull Diameter 0.3-0.6cm Length gt15m
WETMDLL
Bankfull Diameter gt30cm Length gt3-6m
30_MED
Bankfull Diameter gt30cm Length gt6m
30_LON
Bankfull Diameter 0.6-0.8m Length gt15m
WETLDLL
Bankfull Diameter gt0.8m Length gt15m
WETXDLL
Above Bankfull Diameter 0.1-0.3m Length 1.5-5m
DRYSDSL
Above Bankfull Diameter 0.3-0.6cm Length 1.5-5m
DRYMDSL
Above Bankfull Diameter 0.6-0.8m Length 1.5-5m
DRYLDSL
BURPTAC, 1999
Above Bankfull Diameter gt0.8m Length 1.5-5m
DRYXDSL
Above Bankfull Diameter 0.1-0.3m Length 5-15m
DRYSDML
Large Woody Debris (BURPTAC, 1999)
Above Bankfull Diameter 0.3-0.6cm Length 5-15m
DRYMDML
Above Bankfull Diameter 0.6-0.8m Length 5-15m
DRYLDML
Above Bankfull Diameter gt0.8m Length 5-15m
DRYXDML
Field Name
Attribute Name
Above Bankfull Diameter 0.1-0.3m Length gt15m
DRYSDLL
Bankfull Diameter gt10cm Length gt1m
LOD
Above Bankfull Diameter 0.3-0.6cm Length gt15m
DRYMDLL
Above Bankfull Diameter 0.6-0.8m Length gt15m
DRYLDLL
Above Bankfull Diameter gt0.8m Length gt15m
DRYXDLL
30
IV. Protocol Manager Demo