Welcome to the DoD AKN User Guide!

Throughout this page, you will find helpful tips to guide you as you explore and utilize the Avian Knowledge Network!

Choose your topic of interest from the links below.

Not finding the information you need here? Email the DoD AKN Program Team: DoDAKN@erdc.dren.mil

If you run into issues or have any questions, reach out to DoDAKN@erdc.dren.mil

Keep in mind- this guidance will be updated periodically to ensure the most up-to-date guidance is represented, so check back often for updates!

Getting Started with the AKN

SETTING UP AN AKN ACCOUNT

Note: You need a Project code to create an AKN account. New Users will generally need to attend an AKN training to manage a Project.

  1. To register to become an AKN user, and to find your AKN Project code (as needed), follow the steps on the New Users page on the DoD AKN Portal.
  2. Complete all the steps in the form on the New Users page.
  3. You will receive an email from AKN asking you to confirm your email address.
  4. Once you confirm your email address, an email will be sent to a Project Leader in the AKN Project asking them to approve your Project access request.
  5. Once your Project access request is approved, you will receive an email from AKN (datasolutions@pointblue.org) with a temporary password.
  6. Log into the Biologists app with your temporary password; you will be prompted to change your password.

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HOW TO REQUEST ACCESS TO PROJECTS

If you wish to access additional Project(s), go to the Project Request Page and enter another Project code. An email request will be sent to a Project Leader, who can grant permission for access.

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AKN ROLES AND ACCESS LEVELS

User

Users are granted access to the Biologists app and are able to enter, edit, and review field observations.

Project Leader

Project Leaders are granted access to the Project Manager Toolbox and are able to manage AKN Projects through creating and managing Sampling Units, assigning Researchers and Protocols, assigning the User role to other people, managing Data Sharing Levels, and downloading data and metadata (See Glossary). A Project Leader will also automatically have access to the Biologists and Analyst applications. 

The current Project Leader can assist you in getting Project Leader access, or you can send an email to support@pointbluehelp.zendesk.com for assistance.

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Managing an AKN Project

AKN PROTOCOLS

AKN Protocols

Background

AKN Protocols are broadly categorized into protocol types. The main types of Sampling Protocols in the AKN system include: 

Point Count – A stationary survey conducted at specific points that are part of a collection (or transect) of points for a predetermined amount of time at each point, often within a specified distance, exhaustively collecting species that are in your list of survey species (we assume all species not recorded were absent), and individual animals counted once. 

Area Search – Survey within a predefined boundary for a recorded amount of time, exhaustively collecting all survey species that are detected in that boundary, and individual animals counted once. 

Linear Transect – Survey while moving along a path on foot or by vehicle (boat, ship, plane, other) for a recorded amount of time, exhaustively collecting all survey species, and individual animals counted once. 

Secretive Marshbird – Point count with tape playback where focal species are recorded every minute they are detected in a predetermined sequence of calls played in a fixed amount of time. Other non-focal species may also be collected using Point Count methods. 

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Finding the Right Protocol for your Data

Step 1: Check existing Sampling Protocols in the AKN

  • From the Project Manager Toolbox, go to the Protocol Search tool. You’ll have to log in as a Project Leader to use this tool. If you do not have an AKN account, you can create one on the New Users page; or, if you will not be making an AKN account, you can skip to Step 2.
  • Use the drop-down menus and filter features to search through existing Sampling Protocols in the AKN to see if the field protocol you are using fits into an existing Sampling Protocol in the AKN.
  • If you find an AKN Sampling Protocol that matches your field protocol, see How to Add an Existing Protocol to your Project below.
  • If the field protocol you are using closely matches one of the existing AKN Sampling Protocols, but needs a few things adjusted, it may be useful to use that AKN Sampling Protocol as a starting point for describing your Sampling Protocol Definition in Step 2.
Example of an AKN Sampling Protocol Definition

Step 2: If you don’t find a Sampling Protocol that matches your data structure, fill out a Sampling Protocol Definition spreadsheet to describe each of the fields in your dataset. Contact the AKN support team to create a new Sampling Protocol (support@pointbluehelp.zendesk.com).

  • Download and use the DoD AKN Standards: Generic Sampling Protocol Definition Template to provide the field names, descriptions, and acceptable domain values for each field in the sampling protocols​ on the “Field Description” tab.
  • Specify whether the field is a Sampling Event field or an Observation field.
    • Sampling Event fields are fields that describe the entire survey (e.g., date, observer, weather).  ​Many of these​​ ​are ultimately stored in the AKN in “site condition” tables.
    • Observation Event fields are fields that pertain to unique observations within the survey (e.g., detection time, species, distance).
  • An example is provided in the Sampling Protocol Definition Template.

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How to Add an Existing Protocol to your Project:

Step 1: From the Project Manager Toolbox, navigate to the Protocol Manager tool and select your Project.

Step 2: You will then see a list of all the AKN Protocols that are currently in your Project. To add an additional Protocol, click the “Add” tab.

Step 3: Search for the Protocol name that you would like to add. When you locate the Protocol in the list, click to highlight it, and then click “Add Protocol”. You will now see this Protocol on the list of available Protocols when you enter data in the Biologists app and the Bulk Uploader app.

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DESCRIBING FIELD METHODS AND SAMPLING DESIGN

Thoroughly describing field methods prior to submitting data to the Avian Knowledge Network ensures that we maintain a rigorous standard of high-quality data that can be used for analysis and decision support tools. The following standards for describing field methods are for field protocols that have not already been described within the AKN. To check which Protocols are already described in the AKN, go to the Protocol Search tool (Project Leader access required).

Below is a questionnaire that can be used to capture the methodological metadata necessary to understand the methods and assumptions behind your data. This is helpful for when you are planning a new project.

From the AKN Glossary:

Metadata: Metadata are a critical component of data preservation. Metadata provide complete documentation of methods, location, and effort used in collecting the data. Metadata also document specific definitions for data fields and dictionaries for each field’s domain. Data sharing levels are also documented as part of a dataset’s metadata. Metadata are needed to ensure the data can be properly understood and their quality and potential usefulness assessed. Data for which there are no associated metadata have limited utility.

AKN Questionnaire for New Projects

  1. Please provide a short summary of the scope of your project. What are the objectives/questions for your project?
  2. If you know the AKN Sampling Protocol Definition(s) that you will use for your data entry, please provide that information here.
  3. Have you identified Sampling Protocol Definition(s) that are close to your field methodologies, but don’t fit exactly? If so, please provide that information here (If you don’t know, leave this blank).
  4. Briefly describe your field methods. List the citation of the field methodologies used and a URL link if available. Provide your written field protocol or standard operating procedure if it is not available online. Attach a copy of your field form.
  5. How do you select your sampling locations? Briefly describe your study design.
  6. Are you surveying for specific species, if so what? Please specify whether these are the only species you record on your surveys or whether you record all species you observe.
  7. What is the date range (month and years) your surveys took/or will take place? 

If have any questions about survey methodology or planning new projects, you can book an Office Hours appointment with our team and/or reach out to us at DoDAKN@erdc.dren.mil

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CREATING AKN SAMPLING UNITS

Background 

  • Sampling Units are field locations where research or a survey is conducted and samples (observations) are collected (i.e. location data). 
  • There are many types of Sampling Units which are structured in a hierarchy beginning with a Study Area. A Study Area is used to group Sampling Units, and can be used to either identify a geographic location or to group similar surveys.
    • Study Areas can contain multiple types of Sampling Units, including point count transects, area search plots, linear transects, and many other types of Sampling Units, as well as other Study Areas.  
      • NOTE: Study Areas are often thought of as geographic spaces, however in the AKN, Study Areas can be used to group Sampling Events by area, data type, survey project, etc… (e.g.: Project – Fort Carson, Study Area – Breeding Bird Survey Point Counts). Feel free to reach out to the DoD AKN team for questions or advice on how to organize your Sampling Units!
  • Every Sampling Unit in the hierarchy has a Short Name, a Long Name, a Type (e.g., Point Count Point), and a GIS feature that can describe the location. The combination of Short Name and Long Name must be unique within your entire Project.
  • The Short Name will be seen the most throughout the tools and is the shorthand name for a sampling location. The Long Name can be the same as the Short Name or can be made more descriptive if that is useful.
  • It is best practice to have unique Short Names in your Project.
Example plan of a Sampling Unit hierarchy.

Options for Uploading Sampling Units into the AKN

Option 1: Create Sampling Units through Sampling Unit Manager

Option 2: Providing Sampling Units in AKN Format ready for bulk uploading by AKN support staff

Option 3: Uploading Sampling Units Through Bulk Uploader

Sampling Unit Bulk Upload Templates

Following the guidance below (Options 2 and 3), download and populate this Sampling Unit Bulk Upload Template to establish the names and locations of your Sampling Units. Templates for different Sampling Unit types are included in different sheets of this workbook.

Option 1: create Sampling Units through Sampling Unit Manager Tool

Option 1: create Sampling Units through Sampling Unit Manager

AKN Account Required: Yes (see Setting up an AKN Account)

AKN Role Required for Access: Project Leader (see AKN Roles and Access Levels)

  1. From the Project Manager Toolbox, go to the Sampling Unit Manager tool under “Create and manage project metadate”. You’ll have to log in as a Project Leader to use this tool.
  2. Locate your Project in the white box on the left. Use the blue arrows in the Sampling Unit hierarchy to expand and collapse Sampling Units.
    • Select the Sampling Unit where you’d like to nest your new Sampling Units (select the bubble next to Sampling Unit name).
    • If there are no Sampling Units in your Project, simply select the bubble next to your Project name.
  3. Under the “Create” option on the right, you can either:
    • Upload Sampling Units one at a time through the “Online Form“, or
    • Upload multiple Sampling Units at once as long as they are the same Sampling Unit type (e.g.: all area search plots) with a zipped shapefile through the “Shapefile” option. If you are uploading more than a few Sampling Units, it is suggested to do this with a shapefile or KML.
  1. If using the “Online Form” option, select the “Type of Sampling Unit” and enter the Sampling Unit Long Name (“Create a name for this sampling unit”) and Short Name (“Give this sampling unit a short name”).
    • You can then add a description or URL linking to more information.
    • Use the “Digitize Location” tool to enter a location.
    • Continue this process to build out your Sampling Unit hierarchy. For example, if you are uploading point count locations they should be nested as follows:
  1. If using the “Shapefile” option, select the “Type of Sampling Unit” and choose a zipped shapefile to upload.
    • When using the “Shapefile” option, it is best to add Sampling Units within an existing Sampling Unit hierarchy (e.g.: Study Area, Point Count Transect), and populate additional “child” Sampling Units using a shapefile.
    • Note that you will only be shown the Sampling Units types that can be added under the Sampling Unit you have selected from the white hierarchy box on the left side. If you attempt to add Sampling Units (e.g. point count points, area search plots) to a Sampling Unit that is not the correct type, you will not be able to add the shapefile. To check a Sampling Unit’s type, select the bubble next to it, and Type will be displayed on the right.
    • Files will need to use the WGS-84 geographic coordinate system (EPSG:4326).
    • After you select a shapefile and click “Next”, you may populate a prefix for the Long Name and Short Name (optional). You will need to indicate which attribute column from your shapefile corresponds to the Short Name and Long Name, to which the prefix (optional) will be added.

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Option 2: Providing Sampling Units in AKN Format Ready for Bulk Uploading by a Project Leader

Option 2: Providing Sampling Units in AKN Format ready for bulk uploading by a Project Leader

AKN Account Required: No (see Setting up an AKN Account)

AKN Role Required for Access: N/A (see AKN Roles and Access Levels)

If you do not have an AKN account or do not have Project Leader access, below are instructions for preparing your Sampling Units so that they can be uploaded to the AKN Project by a Project Leader. A step-by-step guide to preparing your data can be found below.

Step 1: Provide a Spreadsheet with Locations and Sampling Unit Hierarchy

  • Populate a csv file with the following fields. A template is available for download below (See Sampling Unit Bulk Upload Template) and can also be downloaded directly from the Bulk Uploader by selecting “Get a blank Template to Fill out” Under “Choose what you want to accomplish” (see Option 3 for more on using Bulk Uploader). See Creating AKN Sampling Units – Background for more information on Sampling Units.
    • Study Area Short Name 
      • Required, no spaces
    • Study Area Name
      • A longer, descriptive name that can be the same as Short Name or contain more detail 
      • Not required, but will ensure your Sampling Unit loads properly 
      • Must be unique to the Project when in combination with the Short Name  
    • Point Count Transect Short Name 
      • Required, no spaces
    • Point Count Transect Name
      • A longer, descriptive name that can be the same as Short Name or contain more detail 
      • Not required but will ensure your Sampling Unit loads properly 
      • Must be unique to the Project when in combination with the Short Name  
    • Point Count Point Short Name 
      • Required, no spaces
    • Point Count Point Name
      • A longer, descriptive name that can be the same as Short Name or contain more detail 
      • Not required but will ensure your Sampling Unit loads properly 
      • must be unique to the Project when in combination with the Short Name
    • Latitude 
      • In decimal degrees, WGS 84 datum
    • Longitude 
      • In decimal degrees, WGS 84 datum
  • There will be columns to populate the Study Area name so the tool knows where to put the Sampling Units. You can choose to place all of your Sampling Units into one Study Area or create multiple, depending on your Project.  
  • Build out your Sampling Unit hierarchy nested appropriately for the AKN. For example, if you are uploading point count locations they should be nested as follows: 
  • What makes an AKN transect?
    • Transects are collections of points that get analyzed as statistical replicates.
    • If points are sampled together (sampled as a whole route) then they are not independent of one another, and all points should be nested together under one transect in AKN.
    • If points are individually sampled (not sampled as a whole route) then they are independent of one another, and each point should be nested under a unique transect (i.e., single-point transects).

Step 2: Create a shapefile with Sampling Units

  • This step is optional and not necessary if the coordinates of your points are populated in the Sampling Unit Bulk Upload Template; however, it is an important step for uploading Area Search plots.
  • The geospatial file should include only data for locations for where surveys look place, i.e. points for point counts, polygons for Area search plots, or lines for linear transects.  
  • Must use a WGS-84 geographic coordinate system (EPSG:4326) with coordinates in latitude/longitude
  • Must be 2D (3D shapefiles are not currently supported)
  • Attribute table should contain: 
    • Sampling Unit Short Name
    • Sampling Unit Long Name

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Option 3: Uploading Sampling Units Through the Bulk Uploader Tool

Option 3: Uploading Sampling Units Through the Bulk Uploader Tool

AKN Account Required: Yes (see Setting up an AKN Account)

AKN Role Required for Access: Project Leader (see AKN Roles and Access Levels)

See Creating AKN Sampling Units – Background for more information on Sampling Units.

To use the Bulk Uploader tool to upload Point Count Sampling Units:

  1. From the Project Manager Toolbox, go to the Bulk Uploader tool under “Get observation data in”. You’ll have to log in as a Project Leader to use this tool.
  2. Select your Project (you will only see Projects that you have access to). 
  3. Choose the Add Sampling Units tab and select “Point Count”. 
  4. Populate a csv file with the following fields.  A template is available for download below (See Sampling Unit Bulk Upload Template) and can also be downloaded directly from the Bulk Uploader by selecting “Get a blank Template to Fill out” Under “Choose what you want to accomplish”. See Option 2, Step 1 for details on populating the template.
  5. Once you’ve populated the csv template, click ” Bulk upload datafile” under “Choose what you want to accomplish”. Choose your populated csv file to upload. After successfully selecting a file, the name of the file will appear on the screen. 
  6. If you have a GIS file ready that defines the area of your sampling unit, that can be uploaded as well. This can also be added later. 
  7. Click the Process Sampling Units button. Errors, successes, and information about the batch run will be shown. If there were problems with the file, they will be identified in the error messaging. 

To verify that the points uploaded correctly:

  • From the Project Manager Toolbox, go to the Project Downloader tool under “Download data”.
  • Locate the Project in the white box on the left-hand side, and click the blue arrow to open the Sampling Unit Hierarchy – this should now reflect the organization you just created.
  • If you added geometry to your Sampling Units values, click the box next to your Project name to select all, and download GIS data to either ESRI shapefile or Google Earth (KML), and open the file in a GIS tool to make sure they are located and labeled correctly. For more on downloading Sampling Units, see Downloading Sampling Units from Project Downloader below.

To review previous batch loads for your project, select Batches, then click on an individual batch to expand the details.

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Getting Data into the AKN

ENTERING DATA DIRECTLY USING THE BIOLOGISTS APP

Entering Data Directly Using the Biologists App

  1. Go to the Biologist application
  2. Select the project which you want to enter data for.  
  3. Under “Project Observation Type” select the type of data you are entering. 
  4. Select the sampling unit you are entering data for (e.g. the point count transect or area search plot). If there is a long list of sampling units, use “CTRL-F” to open the search bar and type in the sampling unit name to find it quickly. 
  5. Use the drop-down under “Observation protocol” to select the protocol you are using, if there are multiple and you are unsure check with a Project Leader as the protocol selected will change which data you can enter.  
  6. There may or may not be a site condition protocol to select as well.  
  7. Click Start.  
  8. The data entry will vary depending on the protocol used but you will want to fill out each field and click “Save All” 
    • Fill out the general information of date when the survey took place, start and end time, visit number (leave as None for species checklist), observer’s name, # of other observers, data sharing should say Raw at this point. Note some of these fields are depended on the data type you are working with.  
    • For point count protocols, it will ask you to select the point that you surveyed. To select all, check the top box.  Entered the start time for each point, end times should automatically populate based on the protocol selected. 
    • Enter the site condition fields, if applicable, at the top of the page 
    • Under Observations, Point, select a point from the drop-down menu. 
    • Time should automatically populate with the point’s start time.  It will update if you select a different time bin from the “Time Bin” field. 
    • Enter species codes using 4-letter codes.  If you are unsure of a species code, use the “species lookup” tool linked at the top of the page 
  9. The database is structured to flag errors, if errors pop up edit the referenced data and try to save again, once all errors are fixed the data can be saved.  
  10. After the data are saved you will be taken to the “Proofing page”, here you should review what you entered. Any field with a small vertical blue line can be edited right there, just double click, edit the field, and it will automatically update. Once the data have been reviewed select “Proofing Complete”. 
  11. You can now move onto the next location you wish to enter data for. When you are ready to enter your next route or checklist you can go back by selecting Location on the top of the screen, this will take you back to the list of routes and you will start the process over from step 4. 

Basic Data Entry Guidelines 

  • Enter all data in capital letters, using the “Caps Lock” function on the keyboard. 
  • Enter all data exactly as they appear on the field form. 
  • You must be familiar enough with the Data Entry Form to know which fields are required and which are permitted to be blank. If you are not certain, review this with the Project Lead prior to data entry. Some fields are intentionally left blank and should be left blank during data entry.  
  • Time fields are 24-hour time. 
  • “Tab” is an especially useful shortcut key to move forward from one field to the next. 
  • When entering data, try to leave enough time to complete a block of data (e.g., a point count route). Do not partially enter a point count route, wait until you have entered the entire route to click “Save All” 
ENTERING DATA DIRECTLY USING THE BULK UPLOADER TOOL

Entering Data Directly Using the Bulk Uploader Tool

Option 1: Providing data in AKN Format ready for bulk uploading by AKN support staff

Option 2: Format and Bulk Upload Data as Project Leader

Option 1: Providing data in AKN Format ready for bulk uploading by AKN support staff

Step 1: Prepare appropriate metadata tables

  • Before observation data can be uploaded, a sampling protocol definition should be established for the data structure and sampling units should be uploaded into the project. Use “DoD AKN Guidance: Creating AKN Compatible Sampling Units” and “DoD AKN Guidance: Describing Sampling Protocol Definition” to complete these steps before preparing observation data.
  • Once your Sampling Protocol Definition has been created AKN staff will provide a blank CSV template for how your data should be structured.
  • A separate CSV should be submitted with the researchers names, first name should be in column A and last name should be in column B. A CSV template can be provided as well.

Step 2: Proof and format your data

  • In your data management program (e.g., Access), make sure to identify and clean up any errors prior to submitting your data. Make sure that each value recorded matches the domains outlined in the Sampling Protocol Definition, an error will be triggered if values outside of the sampling definition are used and the data will not upload.
  • A template will be provided that all clean observation and event data should be formatted to
  • Clean up common mistakes (e.g. text entered into numeric fields).
  • All dates and times should be in a single format.
  • Observer names should match the exact spelling in the list submitted and should all be in the same format (e.g. first, last).
  • Make sure the sampling unit names are written exactly the same as the sampling unit names uploaded.

Option 2: Format and bulk upload data AS PROJECT LEADER

You must have an AKN account and Project Leader access to bulk upload data.

Step 1: Prepare appropriate metadata tables

  • Before observation data can be uploaded a sampling protocol definition should be established for the data structure and sampling units must be uploaded into the project. Use “DoD AKN Standards: Format for AKN Compatible Sampling Units” and “DoD AKN Guidance: Describing Sampling Protocol Definition” to complete these steps before preparing observation data.
  • You will also need to upload the researchers names, this includes any name listed as an observer in the database.
    • Select your project in the drop-down menu and click “Add Researcher”
    • Select “Get a blank template to fill out”, download it then populate and save the CSV
    • Select “Bulk upload this datafile”, choose your saves CSV, and select “Process Researchers”
    • If errors pop up, edit your CSV appropriately and try again

Step 2: Proof and format your data

  • Make sure that each value recorded matches the domains outlined in the Sampling Protocol Definition, if values outside of the sampling definition are used they will error and not upload.
  • You will need to format your dataset into a template customized for the sampling protocol definitions used in your project. All data, both event and observation will be uploaded in a single CSV.
  • Download the template in the Bulk Uploading tool under “Add Observations”, “Get a blank template to fill out”. There you will select your data type and sampling protocols used and download the CSV.
  • Structure your dataset to match this template and carefully proof the dataset.
    • Make sure the sampling unit names are written exactly the same as the sampling unit names uploaded
    • Observer names should match the exact spelling in the CSV of uploaded researchers and should all be in the same format (e.g. first, last).

Step 3: Upload data

  • The Bulk Uploader tool uses YAML language to map the data, you will need to download and save the YAML script specific to the sampling protocol you are using. In the tool under, “Add Observations”, “Get Blank Template”, make sure to select the correct sampling protocols then select “Download YAML Template”. As long as all of the field names match the data template this YAML script should not need to be edited.
  • Select “Bulk Upload Dataset”, select the populated data template and the YAML script you just downloaded and select “Process Observations”.
  • It is possible that some data will upload and some will error, if an error message comes up fix the associated data and try to reprocess.

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Getting Data out of the AKN

Data stored in the AKN can be downloaded in two ways, both of which require an AKN account:

DOWNLOADING OBSERVATION DATA FROM PROJECT DOWNLOADER

Downloading Observation Data from Project Downloader

If you have Project Leader access, you may use the Project Downloader tool to retrieve data.  

  • Project leaders can download the data in their AKN Project at any time, no matter what Sharing Level it is assigned to.  
  • Project Downloader allows a Project Leader to download data from one or more Projects at a time. Downloading data from multiple Projects at once in Project Downloader will give you separate files for each Project and each Sampling Protocol.
  • These data will include all fields described in the Sampling Protocol, including the full dataset, not the smoothed data that is stored in the Data Warehouse (see Downloading Warehouse Data from Multiple Projects below), so it will include all extended fields, original distance bins, etc…
  1. From the Project Manager Toolbox, go to the Project Downloader tool under “Download data”. You’ll have to log in as a Project Leader to use this tool.
  2. On the left side, you’ll see a list of Projects.  Click the blue arrow icon next to your Project to see the list of Sampling Units nested underneath.  
  3. Click on the box next to the Sampling Units you wish to download.  Sampling Units nested underneath your selection will automatically be selected.
  4. On the right, under “Observation data”, select the types of survey data you would like to download (e.g., point count observations, area search observations). You can select multiple survey types at a time. Note that these will be delivered in separate files.
    • Try clicking “KML” to download a .kml file.  This is a format that can be uploaded to most GPS units.  Alternatively, if you just want to see a list of your points and their coordinates, click on the “CSV” button to download a spreadsheet with your information. 
  5. You then have the option to filter by date (year-month-day), or you can leave the date filter blank.  
  6. Scroll to the bottom of the page and click “Download”.
Project Downloader screenshot
Example of a CSV download

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DOWNLOADING WAREHOUSE DATA FROM DATA DOWNLOADER

Downloading Warehouse Data from Data Downloader

The Data Downloader tool can be used by anyone with an AKN account and provides access to the “Warehouse” version of the data. This includes any data that is accessible at Sharing Level 5 and any data for Projects in which you are a Project Leader (access to data set to any Sharing Level).

From the AKN Glossary:

Warehouse data: Warehouse data has been formatted to fit a standard format that allows for data collected with different Protocols to be analyzed together.  Warehouse includes all core fields (e.g., species, count, time) and some “smoothed” fields.  For example, distance bins are replaced with averages of the range of the bin to make the data comparable with Protocols that record exact distance. Extended fields are not included in warehouse data.

The Data Downloader tool allows you to search for data based on specific criteria such as Protocol, Project name, species, date, or region. The data downloaded through the Data Downloader tool will only include core fields; it will not include any custom fields that have been created for the Protocol and the information included will be smoothed (e.g.: distance bins converted to their median, and time bins provided as observation times). Instructions for using Data Downloader can be found here:

  1. Navigate to Data Downloader (AKN Account required):
  2. Select the observation type (e.g. Point Count or Area Search) from the tabs at the top. Then, filter for the data you wish to download.  You’ll notice that you have several options: 
    • Protocols—if you know the AKN Sampling Protocol(s) that are relevant to your download.  If not relevant, select “All Protocols” 
    • Date Range—You can either filter by a date range or select “All Dates” 
    • Species—You can select one or more species (select multiple species by holding control and clicking on each species name) 
    • Regions—To filter by region, first select a region type (for example, US States).  Then select the region(s) to filter by.  You can select multiple regions by holding control and clicking on each region name). 
    • Projects—You have the option to download data from all the Projects you are a Project Leader on, plus data from other Projects that is shared at Sharing Level 5.  You can select one or more Projects to download data from here. 
  3. Click “Search” to see a summary of the available data meeting your criteria.
  4. If you are satisfied with your query, click “Download” to download a CSV of the filtered data.

Note that if you do not narrow down your search by using some filters, it will take a very long time to create a download file. 

Data Downloader screenshot
Screenshot of search results in Data Downloader

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DATA SHARING LEVELS

DATA SHARING LEVELS

It is the intention of the AKN that data be shared whenever possible, while carefully considering the tradeoffs between widespread distribution of datasets, the need to ensure data quality and validity, the privacy rights of land owners, and the intentions of the Data Owner(s). AKN, therefore, offers the following data access levels and sharing options that specify which level of access is granted by Data Owners. These are applicable to each and every record in the network individually, so that different records may have different sharing levels.

The AKN encourages its partners to anticipate that most data collected will eventually become part of the public domain. We encourage Data Owners to share data 10 years old or older without restrictions (Level 5). However, the AKN ensures that their data and tools are secure and that access is controlled based on Data Owner intent. 

The following are the Avian Knowledge Network’s Data Sharing Types:

RAW

RAW data are those that are initially input into the AKN that have not been reviewed for accuracy. These data cannot be used in any analysis and are not available in the AKN Data Warehouse for download or the Data Catalog. Data are waiting for either Biologist or Project Leader approval to be elevated to CLEAN. Only the contributing institution has access to data at this level.

CLEAN

CLEAN data are those inputted into the AKN that have been reviewed for accuracy and accepted as valid. The data will be copied into the AKN Data Warehouse for download by those affiliated with the project via the Data Downloader. The data are also available for use by the AKN Analyst Tool. The data are waiting for Project Leader approval for elevation to higher sharing levels. Only project members have access to data at this level.

APPROVED

APPROVED data are available for use by the contributing institution (those associated with a project at the Analyst, User, and Project Leader roles). Data are copied into the AKN Data Warehouse for download by those affiliated with the project.

RESTRICTED

RESTRICTED data are for Projects where information about the Project associated with the data records is made available in the Data Catalog. However, information about restricted records is not shared with the Data Catalog or any other AKN tools. Only the contributing institution has access to data at this level.

Data published under one of the four Data Sharing Levels below are stored in the AKN’s primary data warehouses.

LEVEL 1 – Metadata Only

Metadata about Level 1 records are made available in the Data Catalog, including contact information, locations, survey methods, species surveyed. However, records are not used in any other AKN tools. Only project members have access to data at this level. [Not recommended for DoD data]

LEVEL 2 – Summarize Only

Level 2 inherits all Level 1 rules, and summaries of the data are used to inform data visualization tools, such as the RAIL and Observation Map. The summarized data does not include specific count, Project association, or survey details. Raw data is not shown.

LEVEL 3 – Share with Permission

Level 3 inherits all Level 2 rules and serves strictly as an opt-in “expression of interest” to the broader AKN community. It indicates that the data owner may be open to sharing data sets with partners after establishing permission (e.g., through a data sharing agreement). Selecting Level 3 does NOT automatically transmit, export, or expose any raw data.
[Preferred data sharing level for DoD data]

LEVEL 5 – Share Openly

Level 5 allows full observation data and metadata detail to anyone for use without the need for explicit permission from the data owner.

For full details on Data Sharing in the AKN, see the AKN Website Data Sharing page.

HOW TO SET DATA SHARING LEVELS

HOW TO SET DATA SHARING LEVELS

Project Leaders have the option to share data at multiple levels. Data Sharing Levels are set for each Sampling Event, so you can choose to have specific surveys shared openly and keep others more confidential. Once data is clean, unless there is a sensitive species or other issues that warrant keeping data restricted, DoD suggests most data should be shared at Level 3 and above.  This will allow summaries of your data in the AKN that feed tools such as the Observations Map and the RAIL Tool. 

When you enter data and complete the proofing process, your data are automatically moved from RAW to CLEAN.  After that, you must update Sharing Levels by going to the Set Data Sharing Levels tool, found under “Review and set sharing levels” in the Project Manager Toolbox.

To set data sharing levels: 

  1. From the Project Manager Toolbox, go to the Data Sharing Levels tool under “Review data and set sharing levels”. You’ll have to log in as a Project Leader to use this tool.
  2. Use the drop-down box to select your Project  and click “Go”.
  3. Under “Available Protocols” click on the Protocol type of the data for which you wish to set Data Sharing Levels. 
  4. If necessary, use the date and search filters on the right-hand side to find the events you want to change. Or click on the column headings to sort the Sampling Events by date, location name, etc.
  5. Once located, click on the events you wish to change. You can select multiple events by using CTRL+ Click.
  6. With your events highlighted, use the drop-down menu at the top to select a Data Sharing Level.
  7. Click the “Set” button.  You’ll notice that the Sharing Level has been changed on the events you highlighted. 
  8. If you are satisfied, click on the “Save” button to update the database. 
Data Sharing Levels tool screenshot
METADATA

METADATA

Metadata are a critical component of data preservation. Metadata provide complete documentation of methods, location, and effort used in collecting the data. Metadata also document specific definitions for data fields and dictionaries for each field’s domain. Data sharing levels are also documented as part of a dataset’s metadata. Metadata are needed to ensure the data can be properly understood and their quality and potential usefulness assessed. Data for which there are no associated metadata have limited utility.

DATA USE AND TERMS

DATA USE AND TERMS

The AKN encourages and facilitates the ethical and courteous use of data among collaborators. All cooperators who contribute to and/or access data from the Avian Knowledge Network are required to explicitly agree to these data-sharing terms and policies. 

The use of data, and the publication of results derived directly from those data, are the primary responsibility and privilege of the Data Owner. This privilege is extended to third parties as a contribution by the Data Owner. Data Owners should always be acknowledged in publications and reports.  

Requests for the use of data should be made in writing (via letter or email). The written request should have clearly defined objectives, and should explicitly spell out the terms, conditions, and parameters of the data requested and how they will be used. Data Owners may set individual terms and conditions for allowable use of their data (e.g., acknowledgment, co‐authorship in publications) that may be specified in a Data Sharing Agreement. A suggested general guideline is that, when 20% or more of the data for a publication or report come from one Data Owner, that Owner should be given the opportunity for authorship on the publication or report.

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USING THE OBSERVATION MAP

Using the Observation Map

The Observation Map lets you explore survey locations and data from multiple sources (AKN, North American Breeding Bird Survey (BBS), or eBird) and examine species occurrence and trends. Unlike the Rapid Avian Information Locator (RAIL) tool, the data source and exact location of observations can be identified for data that has been set to Level 2 sharing and above. This tool does not require an AKN account.

  1. Navigate to the Observation Map.
    • From the DoD AKN Portal, click on the “Manage Data Now” button on the home screen.  Scroll down to the heading “Explore Data” and click on “Observation Map”.
  2. Let’s start by getting oriented to the Observation Map: 
    • To zoom in/out, scroll with your mouse, or click on the four arrow icon in the bottom right corner of the map and use the Plus/Minus icons that appear. You can also double click the mouse to zoom in.
    • To pan, click-hold the mouse and drag, or click the four arrow icon in the bottom right corner of the map and click the arrows that appear.
    • “Search by address” (top right corner) lets you zoom into a specific area by name.  Type in a place name and click Go. 
    • Choose a species – the tool requires you to pick a specific species first. Pick one from the dropdown list, and you will see the data collections turn on. The survey points eventually shown on the map will be only those that have at least one observation of this species.
    • Choose a date range – use this if you want to further filter the search to be only within a range of months (say the breeding season), or leave as-is to show year-round data. 
    • Choose a data collection – choose from the AKN (data from the data warehouse), eBird, and BBS collections.  Dots will appear showing where observations were made for that species, and colors indicate which dataset the observations are coming from.  Note that some of the larger collections (e.g., eBird) are broken into regional datasets for system performance. Select the region most relevant to the location you are interested in viewing.
    • Click on a dot on the map – this will give you information about what was observed at that survey location in the panel to the right.
      • If a year is listed at the top, you can click on it to see a summary of that year. 
      • Avian Data Summary – for AKN or BBS data only, click on this link to get an Analyst report of species richness for this location. (Be patient letting this live analytics report run.  You’ll see a twirling icon in the upper left corner while it is running.) 
      • Species – for AKN or BBS data only, click on a species link to get an Analyst report of phenology and species abundance by year.  Again, be patient in letting this live analytics report run. 
    • Choose a map overlay – for visual appearance and area summary. Choose the type of area (e.g. States, Counties, Watersheds) you are interested in summarizing, and click inside a specific area between the observation dots to summarize the entire area.  You will get a summary of observations for that area in the right panel. Note, state summaries take several minutes to run and load.
Screenshot of the Observation Map tool
USING THE RAPID AVIAN INFORMATION LOCATOR (RAIL) TOOL

Using the Rapid Avian Information Locator (RAIL) Tool

The RAIL tool is available without an AKN account. This is a good starting point for finding species information, including PIF population estimates, conservation status, and phenology for any location in the continental U.S. While not intended to provide final data for reports, it can help you find some general information about the species in a particular area and their conservation status.  

Note about the data in the RAIL tool: The species lists you get in the tool are based on an analysis of data from the AKN at sharing level 2-5 along with other datasets, such as BBS and eBird. It is important to understand that the data presented here is modeled on a 10-km grid, so the species list won’t necessarily be exactly tied to the geographic boundary you have drawn—it may include more species than you would expect, or it may exclude species you know are there because they were not abundant in the datasets used for the analysis. Also note that all subspecies are grouped at the species level in this tool.

  1. Navigate to the Rapid Avian Information Locator (RAIL) tool.
    • From the DoD AKN Portal: Click on the “Manage Data Now” button on the home screen.  Scroll down to the heading “Make Decisions” and click on the RAIL tool.
  2. Let’s start by getting oriented to navigating the map and selecting in the RAIL Tool.
    • To zoom in / out, click on the Plus/Minus icons at the top of the screen.  You can also Double click the mouse to zoom in and Shift-Double click to zoom out. 
    • To pan, click-hold the mouse and drag.
    • To change the underlying base map, click on either the Topo or Satellite options in the upper right corner. 
    • Go to location – you can type in an address or place name, hit Enter, and the map will zoom to that location. 
    • Select Area – this lets you draw a polygon on the map, ending that polygon entry by double clicking to close or by clicking again on the first point.  As soon as the area is defined, the Get Results button becomes available. 
    • Use all available species – this lets you select specific species to query. The default is all available species, but you can type species names or codes into this box to query for a list of specific species. You can type in multiple species to create a custom list. 
    • Get Results – this will load the RAIL report on species you chose found in the area you drew.  Click on FILTER RESULTS button at the top of the report to filter species by a variety of characteristics.  Click on the expand button at the right side of any row to get full description about this species, including PIF population estimates, physical characteristics, habitat, biology, conservation status, picture, distribution map, and AKN phenology graph. 

About the RAIL tool – For more information on the underlying data sources and analysis assumptions, see https://avianknowledge.net/index.php/about-rail/.

USING THE ANALYST TOOL

Using the Analyst Tool

  1. You must have an AKN account and have been granted access as a Project Leader to use this tool. It is also important to note that data must be saved higher than sharing level CLEAN to be used in the Analyst tool. 
  2. Log into the AKN as an Analyst.
  3. Select the type of data you will be analyzing.  
  4. Select the project(s) you want to analyze data for, you can analyze data for multiple projects at once.  
  5. At the top you will see “Groups”, this likely does not apply to your project and can be left blank.  
  6. Under Step 2, select the sampling units you would like to analyze. If the project contains a large amount of data not all tools will run, if this occurs you can limit your data by selecting a lower level of sampling unit (or changing other criteria).  
  7. Step 3 choose the criteria such as date range for the data you would like to analyze. Distance is automatically set to be within 50 meters and Flyovers are set to be excluded, both of these settings can be changed.  
  8. You can leave the Select Groups blank unless this pertains to your project. 
  9. Select either All Species or the species you would like to analyze, you can select more than one by holding the Shift key.  
  10. Select the type of Analysis you would like to run.  

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AKN Glossary for DoD

AKN GLOSSARY FOR DOD

AKN Glossary for DoD

AKN Roles

(Note: to obtain any level of access in the AKN, you must first register for an AKN account. Please visit the New Users page to find your Project name and create a new account.)   

The AKN allows for multiple levels of access to enter, manage, and share data. AKN users are assigned a Role associated with each AKN Project they have permission to access. Current AKN Roles include: 

  • User: An AKN account assigned to the Role of “User” in an AKN Project can enter and proof data. Users can also review, edit, or correct previously entered data in any dataset housed within the AKN Project until the Sharing Level of the data has been set beyond “CLEAN”. 
  • Project Leader: In addition to all User Role capacities, AKN accounts assigned to the Role of “Project Leader” in an AKN Project can assign Sampling Protocol Definitions to the AKN Project, manage the Sampling Units (areas, points, transects, etc…), manage data, get full exports of the AKN Project data from the system, and manage the Roles (User or Project Leader) of other AKN accounts in the AKN Project. Project Leaders can also set the desired data sharing levels for data, which determines how the data will appear in the various tools in AKN.  
  • Unregistered Researcher: For individuals that collect data but are not involved with AKN data entry, management, or analysis, it is not necessary to create an AKN account. Instead, their names can be added to the Project as Unregistered Researchers. A User or Project Leader can enter data on behalf of the Unregistered Researcher. Note that individuals assigned this AKN Role cannot be changed to a different Role. AKN accounts cannot be assigned this Role.

Data Management Terms

  • AKN Project: Fundamental unit of organization for observation data within the AKN. Projects contain information about how (Sampling Protocols), who (Researchers), where (Sampling Units), when (Sampling Events), and what (Sampling Event Observations) data are collected. For DoD, each installation has its own project.
  • Sampling Unit: Field location where research or a survey is conducted and samples (observations) are collected. Sampling units are arranged hierarchically within AKN Projects (e.g. point count points nested within a transect). Sampling Units contain a location name and geometry that describes where it sits on the earth.  All point, polygon and other geographic data are described in WGS-84 Latitude-Longitude (EPSG:4326) geographical coordinate system.
  • Researcher: A person that collects data in the field or enters, manages, or analyzes data in the AKN. All Researchers are assigned an AKN Role (described above) by a Project Leader in each project they receive access to. Researchers can have different Roles in different AKN Projects. Project Leaders can change a Researcher’s Role in the Project at any time. The names of all individuals involved in data collection must be added to the AKN Project as Researchers in order for the data to be entered. Researchers may or may not have an AKN user account.  
  • Sampling Protocol: Defines how the data were collected and how they are stored. This includes extended field names, domains, and any rules built into the data structure.  
  • Sampling Event: Represents the survey itself with a unique combination of location, date and time, person/people, and the protocol employed.
  • Sampling Observation:  Observations made at a Sampling Event; these observations will differ depending on the specific AKN Protocol being used, but will contain some core fields such as species and count.

Sampling Protocol Types

  • Area Search: An observer records all the birds detected (often with other behavior characteristics) within a specific boundary in a recorded period of time. Area search Protocols include start and end times, the species observed, and can also include a count, detection cues, or breeding behaviors.  Area search Protocols are flexible and can be adapted to a wide variety of surveys, and are often used to enter comprehensive species checklists.  Unless specified, the Protocol is assumed to be an exhaustive survey of all species.
  • Point Count: An observer records all the birds detected (often including other behavior characteristics) from a series of known, fixed locations, surveying each location for a set period of time. Point count Protocols include the duration of the survey, how the time is binned, and often include distance (binned or exact), detection cues, or breeding behavior. Unless specified, the Protocol is assumed to be an exhaustive survey of all species and that each animal is counted once.
  • Linear Transect: An observer moves along a path recording all the birds detected (often with other behavior characteristics) along the way in a recorded period of time. Linear Transects are done either on foot or in a vehicle (airplane, boat, etc). Unless specified, the Protocol is assumed to be an exhaustive search of all species.
  • Secretive Marshbird: Secretive Marshbird Protocols follow the Conway National Protocol Framework for surveying species at points using a predefined playback sequence 
  • Site Conditions: Site Condition Protocols are used in conjunction with another Protocol type (Point Count, Area Search, etc) for recording covariate characteristics about the landscape at or around a sampling location at a given date and time. Site Condition fields apply to the entire Sampling Event, not just a single observation or record and can include fields such as weather conditions, vegetation cover, and disturbance.  Site Conditions Protocols can be applied to multiple Projects if desired. 

Data Sharing Levels: Each observation available in the AKN is tagged with a Data Sharing Level as determined by the Data Owner, and set by the Project Leader (the Data Owner may also be the Project Leader). The AKN provides multiple Data Sharing Levels (see the Data Sharing Levels section in this User Guide).  

Core fields: Fields that are automatically associated with a Protocol, either in the event or observation table. Some core fields are required (i.e., set by the AKN) and others are not and can be suppressed so they do not show up on the user interface. Example core fields that are required are species and count.

Extended fields: Custom fields that are specific to your database. Extended fields may apply to a Site Condition Protocol or an observation Protocol. Once created, extended fields can be used in multiple Protocols within the same Protocol type (e.g. area search, point count). Extended fields are included in the Project database and will be part of the data downloaded through the Project Downloader, but will not be included in the AKN tools such as the Data Downloader or the Analyst.

Project data: Project data includes all the data as you entered it into your Project.  This includes all extended fields, the original distance bins, etc… that are included in the Protocol you use. 

Warehouse data: Warehouse data has been formatted to fit a standard format that allows for data collected with different Protocols to be analyzed together.  Warehouse includes all core fields (e.g., species, count, time) and some “smoothed” fields.  For example, distance bins are replaced with averages of the range of the bin to make the data comparable with Protocols that record exact distance. Extended fields are not included in warehouse data.

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