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STREAMNET NEWS

A Newsletter from StreamNet
A Fish Data Delivery Project for the Pacific Northwest
Issue #14 - December 19, 2012
Go to:   Previous newsletter.

Welcome to the fourteenth StreamNet News!

In the time since the last StreamNet Newsletter we have made significant improvements and changes in the data available, your online experience, and the behind-the-scenes programming that makes it possible. This newsletter tells about some of these significant changes. Your feedback is welcome.




Table of Contents

  1. New "Integrated Query System"
  2. New Data in the StreamNet Database
  3. Updated Redband Trout and Pacific Lamprey Distribution for Oregon
  4. StreamNet Data Store News
  5. StreamNet Supporting Coordinated Assessments
  6. Outmigrant Database, Data Entry, QC, and Analysis System Available





1. NEW "INTEGRATED QUERY SYSTEM"

On July 20 our new "Integrated Query System" became available for use. We named it the Integrated Query System because it integrates text-based and map-based approaches to finding data, and simultaneously displays text, map, and graphical representations of the data as output while you use the system to find the data of interest to you. To help you get started we have created a Quick Start Guide.

The Integrated Query System has several new functions and improvements not available in our older "Web Query System."

  • It is possible to select more than one value for a criterion. For example, in the older system you could pick Chinook salmon, or steelhead, or coho salmon, but you had to choose one at a time. The new system lets you pick any combination of values for all of the criteria. That means it is possible, for example, to select all the data at once for 2 species in 3 subbasins.
  • It is possible to sort and filter the data on most columns of interest, making it easier to find data.
  • Some pieces of data not provided by the older Web Query System -- because they were judged too sparse -- are now provided.
  • Some pieces of data not provided by the older Web Query System -- because they were too complex to represent -- are now displayed. This includes data such as creel surveys where data are collected at multiple locations and pooled into a single observation. These data and their multiple locations are displayed in the new Integrated Query System.
  • You can select which pieces of information are shown, and rearrange their display order. We provide a default list of data elements that we anticipate will be of interest to most people, but additional elements not initially displayed are available and can be added to the display. Other aspects of the display are also customizable, such as column widths and how much of the screen is devoted to the 4 quadrants (an explanation of the quadrants is below).
  • The specific locations where data were collected are shown as you browse the data. Now, when you read that data were collected from river mile 18.4 to river mile 23.6 you can see on the map exactly what is meant.
  • You can create your own "Groups," assign data to groups, and then sort and filter by your groups just as you do any other piece of information. For example, you may want to create a group for Chinook salmon counts data in the Willamette Basin and another for Chinook salmon counts in the Yakima Basin. Or you may want to flag data sets you judge to be high priority for your purposes differently than those you judge to be lower priority by assigning them to different groups. Assigning data to groups lets you easily find them when you return the next time, helping you more easily determine if updates are available for data of interest to you.
  • Three data categories have been consolidated in one place under "fish counts." If you are looking for a variety of data types related to fish abundance, this means you no longer have to run separate queries for spawner counts, dam/weir counts, and estimates of spawning populations.
  • The system remembers your customizations, groups, and data filters, and applies them the next time you return. (For this reason -- and to help us understand who our users are -- the Integrated Query System requires that you log in.)
  • Many additional new features are not listed here.

The Integrated Query System looks and functions very differently than our older Web Query System. The new system has a feel of staying in one place rather than moving through a series of steps.

There are 4 main quadrants on the page in the new system. Presented like a spreadsheet in the upper left quadrant is the basic information about a group of data, such as data category, location, species, years, etc. As you change rows in this quadrant the information in the other 3 quadrants changes. Tabs at the top of this quadrant let you change the types of data you are browsing.

In the upper right quadrant is a map that shows where the data were collected. In the lower right quadrant, when appropriate, is a graph of the data set selected. The graph contains some information not immediately obvious. Hover your mouse over a bar in the graph and the year represented by the bar is shown along with the exact value for that year. Years with a count of zero are differentiated from years with no counts (nulls). And in the lower left quadrant is another spreadsheet-like display, this one containing details about the individual measurements such as specific begin and end dates, sampling and calculation methods, number, etc.

The older Web Query System will remain available for at least as long as it takes to fully develop and debug the new Integrated Query System. While we are proud of the new Integrated Query System, we know it is not complete and very likely has bugs and lacks functions that people would find useful. Please let us know how you like it, if you find errors, and if there is anything you would like to see added to the system. Some bugs are still being worked out, such as difficulties with older browsers. Currently Firefox and Chrome work best. Please let us know about any issues you encounter, as it is a work in progress.


2. NEW DATA IN THE STREAMNET DATABASE

StreamNet's main database, and the streams GIS layer ("hydrography") it is integrated with, have seen extensive updates since the previous StreamNet Newsletter. These updates include:

  • 22,200 new locations (mainly small streams) comprising versions 3.0 and 3.1 of our mixed-scale hydrography
  • 1,076 new time series ("trends") related to fish abundance
  • 20,700 new fish count observations
  • 44,300 new or updated barrier records
  • 18,000 new records of species-specific passability at specific barriers
  • 1,600 new dam records
  • 5,400 new fish distribution records
  • 13,800 new or updated fish age records
  • 1,400 new references
  • many other updates.

All these new data are available via the Integrated Query System and the Web Query System. The current mixed-scale hydrography is available on our "Maps & GIS Data" page.

An updated MS Access version of the StreamNet database reflecting all the above changes was posted on the StreamNet website December 5th. This Access database does not have a user interface or dynamic features like those that are part of the StreamNet online Web Query System, the new Integrated Query System, or the interactive mappers. It is primarily intended for use by power users engaged in regional scale analyses and requires significant experience using Access, so most users will find the online systems more suited to their needs. You can find this updated Access database on our Database Download page.

For additional information regarding two of the recent data updates, see the next item, "Updated Redband Trout and Pacific Lamprey Distribution for Oregon".

3. UPDATED REDBAND TROUT AND PACIFIC LAMPREY DISTRIBUTION FOR OREGON

Oregon Department of Fish and Wildlife recently developed a comprehensive state-wide redband trout (Oncorhynchus mykiss gairdnerii and O. m. newberrii) habitat data set to support the range-wide redband trout assessment and also to support the Western Governors Association's Decision Support System.

Previous to this effort, redband trout data had only been mapped in the John Day and closed basins within Oregon. Recently developed redband trout data were compiled from a mix of existing digital and hard copy data sources as well as through a mapping exercise to capture the knowledge of agency biologists. The data set tracks a number of different attributes at the record level including the data originator, the evidence or method used to determine the existence of the species in the indicated reach, habitat use, life history types, origin (indigenous, native, or introduced), and how the population is sustained (natural reproduction vs. planting).

Additionally, ODFW recently compiled observation-based distribution data for Pacific lamprey to support recent fish passage barrier prioritization efforts within the agency.

Both the redband trout and Pacific lamprey distribution data are now available on StreamNet via the new Integrated Query System as well as the traditional Web Query System. GIS layers for these two data sets will be available on our Maps and GIS Data page at about the time you receive this newsletter. They are also available from ODFW at their Natural Resources Information Management Program web site.


4. STREAMNET DATA STORE NEWS

Where can you archive, share, and find fish-related data sets that don't fit in any of the regional standard databases such as StreamNet, the Regional Mark Processing Center, PTAGIS, the Fish Passage Center, or the Pacific Northwest Water Quality Exchange? The StreamNet Data Store!

The Data Store is an excellent place to archive, share, and find fish-related data sets that do not fit any of the standard regional data systems. For example, recent additions to the Data Store include: updated fish population surveys and trout genetics data from Montana Fish, Wildlife and Parks; Yankee Fork salmon restoration project data from the Shoshone-Bannock Tribes; and the data used for an update to the multi-agency Yellowstone cutthroat trout status assessment.

For projects with a contractual obligation to share data sets, the StreamNet Data Store lets you fulfill this requirement quickly and easily. This is becoming more common for projects funded by the Bonneville Power Administration and other funding entities. The Bonneville Power Administration now requires that all data captured by fish and wildlife projects they fund be made available in an appropriate location and be adequately described. With this new requirement we expect a large number of data sets to begin coming into the StreamNet Data Store in the next year. If you are looking for data you will want to check the Data Store occasionally to determine if data sets of interest have been added.

Most people find it a very quick and simple thing to upload their data sets to the Data Store and complete the data set description process. If you are one of the people required to make the data you collect available and you choose to use the StreamNet Data Store, we can help you to complete the process if necessary. Just give StreamNet a call at 503-595-3100 or send us an email and we will help you get the process completed quickly.


5. STREAMNET SUPPORTING COORDINATED ASSESSMENTS

The "Coordinated Assessments" project is a relatively new regional initiative aimed at sharing derived data that are useful as indicators for evaluating the status of fish populations in the Columbia River basin. Whereas many of the data provided by StreamNet are annual summaries of field data collected at specific locations, the focus of the coordinated assessments effort is high-level derived values ("indicators" and "metrics") meant to represent the status of entire populations of fish. Four initial data types related to the Viable Salmonid Population model will be shared: abundance of natural origin spawners; smolt to adult ratios; adult recruits per spawner; and juvenile recruits per spawner.

StreamNet was heavily involved in development and initiation of the Coordinated Assessments project. In 2011 we completed our portion of the initial exploratory phase of the project which was led by Columbia Basin Fish and Wildlife Authority and the Pacific Northwest Aquatic Monitoring Partnership. StreamNet hired ten temporary data specialists who worked within the nine participating state and tribal fisheries agencies to locate the specific indicators and supporting metrics, describe how the data flow from collection through analysis, obtain representative indicators and metrics and descriptive metadata, and assist the agencies to identify data gaps and develop data management strategies.

The data specialists were called together at the end of the effort and developed feedback on the lessons learned from the effort. This information was synthesized and presented to a workshop of all project participants, where it was used to support development of a basin-wide data sharing strategy and formulation of plans for the data sharing phase of the project.

We worked with the other project participants and developed a Data Exchange Standard which describes the specific fields to be shared on an ongoing basis for the four indicators.

We continue to participate in the Coordinated Assessments Planning Group and will continue to provide technical assistance as the effort expands to additional indicators. We also intend to assist agencies as they develop internal data sharing capacities. Such increased data management capabilities will not only serve to facilitate broader sharing of indicators for regional reporting but will also facilitate more efficient use of data internally and speed data updates to StreamNet.


6. OUTMIGRANT DATABASE, DATA ENTRY, QC, AND ANALYSIS SYSTEM AVAILABLE

Under funding provided by the U.S. Fish and Wildlife Service, StreamNet personnel at Pacific States Marine Fisheries Commission, along with other PSMFC personnel and a statistician from Western Ecosystems, Inc., have created a system for estimating the number of fishes migrating in a stream. Intended primarily to estimate the number of juvenile salmonids migrating to the sea, it could also be used for other taxa and for fish migrating upstream. The system provides for data entry, data management, data quality control, and data analysis in order to be able to easily estimate the total number of fish (smolts or other life stages) that pass a trapping site over a defined period of time. The system is nearing completion and currently undergoing beta testing. Some of the features of the system are:

  • A database that stores and integrates data for ...
    • Details about sampling such as
      • site
      • specific trap position
      • sampling conditions
      • times of significant events
      • whether a usable sample was successfully obtained.
    • Details about fish captured such as
      • taxon
      • rearing type
      • size
      • life stage
      • health
      • whether the fish was randomly pulled from the sample or deliberately selected for measurements
      • marks and tags
      • whether the fish is a recapture from a specific release
      • physical samples collected
      • groups of fish for which the above were not specifically determined.
    • Details about releases designed to estimate trap efficiency such as
      • release site
      • release time, and length of time the test is to run
      • targeted recapture site(s)
      • number released
      • number recaptured.
    • Associated environmental measurements
      • stream discharge
      • water temperature
      • turbidity
      • other water quality measures
      • number recaptured
      • release time, and length of time the test is to run.
  • The database prevents many common data integrity errors. It also contains pre-built query templates to help guide creation of ad-hoc queries.
  • A user interface that ...
    • Provides for fast data entry
    • Prevents additional common data integrity errors (additional integrity checks can be added)
    • Automatically matches marked recaptures to the release each is from (and provides feedback if ambiguities are present)
    • Has tools to help integrate data from several sources
    • Is designed for data entry from paper data sheets
    • Makes backups to prevent data loss
    • Has a layout that can be modified to better suit your needs
    • Allows for easy addition of data analysis routines (written in R).
  • Data analysis and graphics routines that, for the site and taxon and range of dates you define, do the following:
    • Provide a point estimate (based on splines) and confidence limits (via boot-strapping) for the number of fish moving past the trapping site (annual or other time frames you define)
    • Estimate numbers of fish for missing sampling times
    • Provide summaries of releases and recaptures, and thus capture efficiency
    • Compute "take" of ESA-listed species
    • Graph size of fish by date of capture
    • Graph length-frequency of captured fish.

The system, which runs on Windows computers, does not need to be formally installed. Simply copy the files to a hard drive and it is ready to use. Export of the data to other systems such as PTAGIS and WDFW's JMX, while not yet developed, is possible.

If you are interested in seeing it in action or giving it a try, please contact Mike Banach by phone at 503-595-3100 or send us an email. We can further discuss the capabilities of the system, provide live demonstrations online, and assist with implementation at your location.




The end.


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COMMENTS on the StreamNet project, its web site, its data products, or your data needs are encouraged and appreciated. Click the "Contact StreamNet" button on any page of the StreamNet web site.

ABOUT THE STREAMNET PROJECT:
StreamNet is a cooperative, multi-agency effort among the Columbia River Basin's state, tribal, and federal fisheries agencies, the Northwest Power and Conservation Council (NPCC), the Bonneville Power Administration, and the Pacific States Marine Fisheries Commission to compile fish-related data. We compile and make available on our web site information intended to be useful to fisheries managers and researchers, land managers, planners, and others. We acquire, regionally standardize, and georeference data from multiple sources on a number of topics, including fish distribution, fish abundance trends, hatchery returns, harvest levels, migration barriers, hatcheries, and dams. We provide a catalog of photographs relevant to fish species and facilities in the region. Through our "Data Publishing Service" and "Data Store" we archive and provide access to stand-alone data sets created by other entities. We maintain a standard GIS hydrography layer for the Pacific Northwest. We maintain the official list of stream reaches the NPCC has recommended be protected from dam construction. We provide pre-made maps and let you make maps interactively from data in the StreamNet database to meet your needs. We continually work to update these resources, so new information becomes available several times each year. We also provide customized data-related services for participants in the NPCC's Fish and Wildlife Program.

You can learn more about StreamNet at http://old.streamnet.org/about.html. We exist in order to bring useful information to people such as you, and we welcome your questions, feedback, and suggestions. We also hope you will inform your colleagues about the resources available at StreamNet (http://old.streamnet.org).



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