PNAMP Protocol Library Focus Group Meeting #2
April 24, 2009
Protocol Manager Demonstration & Walkthrough Tutorial – Creating a Complete Metadata Record
The following demonstration is intended as a quick guide to creating a complete metadata record in Protocol Manager and includes the steps for documenting all aspects of protocol metadata per the standard employed by the software. The walkthrough begins with generating a program and project description, and then walks the user through the process of creating or adding protocols, methods, attributes, and references. Also demonstrated is the reporting functionality, and the ability to export all or a subset of metadata records.
Create a Database
1. Start the FFI Database Managerapplication, select the “Connect” menu item and select “SQL Server…”.
2. Select the SQL Server Instance created during installation and configuration, enter the username and password for this instance, and click “OK”.
3. Select the “Server” menu item, and select “Create Database” > “Protocol Manager”.
4. Give the database a short name, and click “OK” (a command window appears as the database is being created – this will take a few minutes).
5. Expand the SQL Server instance item in the left pane and expand the “Databases” item. The new database should appear in this list.
6. Close FFI Database Manager
Import RM&E Data
1. Start Protocol Manager, enter the username/password, and select the database created in the previous steps – click “OK”.
2. Select the “Database” menu item, and choose “Import”. An “Open” dialog screen appears prompting for a file with a “.pm” or “.pmd” extension. These are XML schemas that include both the structure and the data of a dataset.
3. Navigate to the “FFI_PM_Export.pmd” export file, select it and click “Open”. Click “Yes” at the warning message box.
4. Three existing programs should appear. Navigate through one or more of the programs, and notice the structure of programs, projects, protocols, methods, and method attributes. Right click on any one of these and select “Properties” to view more information such as descriptions, references, etc.
Create a Program
“Program” in the context of the Protocol Manager application refers to a collection of monitoring projects. Usually this is a multi-year administrative body that consists of one or more agencies or organizations.
1. Select the “Programs” menu item and select “New”.
2. Enter a short descriptive name for the program such as AREMP, PIBO, NAWQA, or use the name of an agency or organization.
3. Enter a descriptiveObjective for the program, including the purpose, outcome, and time-frame for the monitoring program.
4. Click on the “Description” tab, and enter a descriptive narrative about the history of the program, what organizations or agencies the program is comprised of, and a mention of the intended uses of the products that are generated by the program (e.g. “A regional database is updated quarterly and can be used in small-scale, large-area analysis of …”).
5. Click on the “Contact” tab and enter the primary contact information of an individual or group whom would be most likely to receive requests for data, answer questions, etc.
6. Click “Save & Close”. The program should appear in the left pane.
Create a Project
1. Right-click on the program created in the previous steps and select “New Project”.
2. Give the project a brief yet explanatory name such as “AREMP Habitat Assessment”
3. Complete the Objective, Description, and Contact information in the same manner as the program information. Note: These descriptions should be specific to an aspect of the program, and should give a general overview of the protocols, methods, and any products or datasets resulting from project implementation. The contact information should also be specific to the project, and could include a project manager, or someone familiar with the specific data generated.
4. Click “Save & Close”. The project should appear within the program created in the previous steps.
Create and Assimilate Methods
The workflow makes a diversion at this point: as one would assume that he or she could create a protocol within a project using the same procedure in the previous steps where we created a project within a program, in practice this will not work. At this point, the user must add an existing protocol that will then be “applied” to the project. This situation also exists for methods in that one cannot create a protocol and start creating methods from scratch. The methods to be included in the protocol must already exist. Therefore, we will jump down a couple of levels in the hierarchy and start by creating a method.
1. Click on the “Methods” tab. Existing methods will show up in the left pane.
2. In the Method Builder, enter a descriptive but short name for the method: usually this is the specific indicator or metric that is being monitored or measured.
3. Select a “Unit System”. This assumes that all of the metrics or attributes collected in this method will be of a single unit system, or a combination of the standard and metric.
4. Select a “Method Shape”. Generally, this refers to the geospatial shape of the sampling or monitoring area such as a point (grab), line, circle, etc.
5. Leave “Single Record” as “False”.
6. By default, the “Sample Attributes” under “Method Properties” already have a series populated with “Visited” as a caption and name. Sample attributes refer to aspects of the sampling or monitoring instance, and might include additional codes and attributes of the sample collection event.
7. Click on the “Method Attributes” tab and click on the button and enter a few attributes for the method. These are generally the metrics that the method collects, and should reflect the information found on a field database entry form. It also may refer to the basic or individual data elements stored by a dataset.
8. Click on the “Description” tab and enter a descriptive narrative for the method. This may include the actual steps in logical order that must be undertaken for appropriate implementation of the method.
9. Click on the “References” tab and click on the “Select References” column header. A list of references appears by type.
10. Under the “Books” tab, click on “New” and fill out all of the citation sections.
11. Click “Save & Close”.
12. Back at the Method Reference Selector dialog screen, select the “Method References” drop-down and select “Assign Reference”.
13. Select the reference and select the “Method References” menu item again. Select “Set Primary”.
14. Add another reference and assign it, but do not select “Set Primary”. Click “OK & Close”.
15. Back at the Method Builder dialog screen, select the “Organizations” tab. Select one or more classifications for this method. Click “Save & Close”.
Create a Protocol
1. Click on the “Protocols” tab. A list of all protocols in the database will appear. Use the filter command buttons to see whether the method created in the previous steps appears under the classifications selected.
2. Turn all filters off and select the “Protocols” menu item.
3. Select “New”. The Protocol Builder dialog appears.
4. Enter a descriptive but brief name for the protocol. Generally, this refers to the topical theme of the monitoring design based on the suite of methods used. It should be a marriage of the project and the high-level or over-arching indicators that answer the project’s objective. An example might a protocol for water quality, one for habitat, and one for fish presence/abundance.
5. Click on the Description tab and provide a general description of the protocol, including an overview of the methods used and perhaps a mention of whether these methods were adopted and modified from other programs or projects.
6. Click on “Contact” and fill out the information as requested. It is not necessary to click on the “Version History” tab.
7. Right-click on the new protocol in the left pane and select “Add/Remove Protocol Methods”.
8. At the Protocol Method Selector, select the method created in the previous steps and click on the “>” button.
9. Select a few other methods and add these to the protocol. Click “Save & Close”.
10. Click on the “Programs & Projects” tab.
11. Expand the program created in the previous steps if necessary, and right-click on the project created previously.
12. Select “Add/Remove Project Protocols” and add the protocol created previously by selecting and clicking on the “>” button.
13. Click “Save & Close”.
Promote Protocols and Methods
Protocols and methods can be edited in Protocol Manager as long as they have not yet been “promoted” from development to production status. Once they are promoted, they can no longer be edited and have to be duplicated in order to make changes. This effectively creates a new method or protocol, thereby adding one level of certainty that a method or protocol has not been changed through time without properly documenting the change.
1. Click on the “Methods” tab and select the method created previously. It will have a yellow and black triangle denoting that it is in “development” status.
2. With the method selected, choose the “Tools” menu item and select “Check for Errors”. If no errors are found, click “Close”.
3. Right-click on the method and select “Promote Method”. Click “Yes” on the warning message box.
4. At the Version Builder dialog, enter a year or range of years denoting when the method was used, or will be used.
5. Click “Save”.
6. Select the “Protocols” tab and select the protocol created previously.
7. With the protocol selected, choose the “Tools” menu item and select “Check for Errors”. If no errors appear, click “Close”.
8. Right-click on the protocol and select “Promote Protocol”. Click “Yes” on the warning message box and enter a descriptive date or range of dates denoting when the protocol was or will be used.
Generate a Report & Export File
1. Select the “Reports” menu item and select “Method Reports”.
2. Navigate to the new method and under “Description” click the “Complete” radio button.
3. Select: “Yes” under “Show Method Version History”; “Detailed - …” under “Show Method Attributes”; “All References” under “Show References”; and “Yes” under “Show Method Organizations”.
4. Click “Generate Report”.
5. Give the report a descriptive name and click “save”. The file created is a flat text file, so it is not necessary to provide a type.
6. Generate another report using the “Program and Project” option.
7. Select the “Database” menu item and select “Export” > “Single Project”. In the Project Selector dialog, select the new project and click export.
8. Name the file similar to the program and project name, and choose save. This will create an XML Schema with the structure, rules, and data from this project. This can then be imported into another Protocol Manager database, or into MS Access, SQL Server, etc.
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