Integrated Pest Managment

Preview

IPM is still in preview - feedback welcome

The Integrated Pest Management (= IPM) in the DiversityWorkbench is designed to support the recording and evaluation of IPM-related data. IPM is organized via Tasks.

The taxon specific data are stored in DiversityTaxonNames.

DiversityCollection allows

  • Monitoring of pests, bycatch etc. in resp. on
    • Traps
    • Collections
    • Fascicles
    • Specimens
  • Recording of
    • Cleanings
    • Treatments
    • Application of beneficials
    • Sensor data
  • Generation of
    • Reports
    • Charts
    • Plans
  • Collection: Handling the collections in the tree
    • Change to top collection: Change to the parent collection of the current top collection
    • Add collection
  • Taxa: Setting the selection of taxa shown in the interface
    • Pests
    • Bycatch
    • Beneficials
  • Settings: Showing additional options to document pests
    • Show pests outside traps
    • Show pests on specimen
    • Show pests on groups of specimen

Data

The tables below the inspection dates contain the results for pests and bycatch. Optionally additional tables for pests on e.g. specimen can be included. The first column shows the group, the second the taxon with a link to resources in DiversityTaxonNames. If you click on the link the available resources will be shown (see below).

Column 3 shows preview of images in DiversityTaxonNames. To see the original image together with additional images, click on the preview image (see below).

The next columns contain the counts of the taxa detected in the traps. The acronyms of the traps within the collection hierarchy are shown in the header. The numbers, states and notes for the taxa detected in the traps are entered here. If you want to add any comment, this must be added after the number, separated by a space. Only valid numbers will be included in the analysis shown in the chart.  

Subsections of Integrated Pest Managment

Integrated Pest Managment

Architecture

---
title: Taxa
---
graph TD;
    DTN(DiversityTaxonNames) -->|Transfer extract of valid data in cache table<br>procFillTaxonName_Cache| CacheTable[Table <u>TaxonName_Cache</u><br>NameID int<br>JSON nvarchar]
    CacheTable --> API
    API --> Lists{separation of data <br>according to Lists}
    Lists --> Pests[Pests]
    Lists --> Bycatch[Bycatch]
    Lists --> Beneficials[Beneficials]
    Pests --> UPests[User selects pests<br>present in collection<br>Selection is stored in app]
    Bycatch --> UBy[User selects taxa<br>that should be recorded<br>Selection is stored in app]
    Beneficials --> UBene[Selected along with<br>application in collection]

Data recording

IPM covers several areas as shown in the mindmap below

mindmap
  IPM
  ::icon(fa fa-bug)
    Lists of Taxa
    ::icon(fa fa-list)
        API: JSON
        ::icon(fa fa-cloud)
            DTN
            ::icon(fa fa-database)
    Floor plan
    ::icon(fa fa-map)
    Prometheus time series database
    ::icon(fa fa-fire)
      Sensors
      ::icon(fa fa-thermometer-half)
    Traps
    ::icon(fa fa-cat)
    Treatment
    ::icon(fa fa-broom)

Taxa

API

The taxon lists are provided by the module DiversityTaxonNames. The data are collected in a cache table and provided via an API as json. The module provides 3 lists.

mindmap
  DTN 
  ::icon(fa fa-database)
    Cache
    ::icon(fa fa-table)
        API: JSON
        ::icon(fa fa-cloud)
            Pests
            ::icon(fa fa-list)
            Bycatch
            ::icon(fa fa-list)
            Beneficials
            ::icon(fa fa-list)

Local lists

The taxa are sorted according to their hierarchy including their stages etc. In the user interface the taxa are grouped according to group defined in DTN that correspond to higher taxa. From every list the user can decide which taxa and their stages, remains etc. should be included in the local list for selection

mindmap
  DiversityTaxonNames containing Taxa 
  ::icon(fa fa-database)
    Cache containing JSON extract of valid taxa
    ::icon(fa fa-table)
        API: JSON
        ::icon(fa fa-cloud)
            Taxa as provided by API
            ::icon(fa fa-list)
                Sorting according to hierarchy
                ::icon(fa fa-sitemap)
                    Local list as selected by the user
                    ::icon(fa fa-check-square)

Plan

The floor plan for the collection provides the position of traps and sensors within the collection.

mindmap
    Floor plan including scale
    ::icon(fa fa-map)
        Rooms within the collection. Calculation of area and volume on base of scale
        ::icon(fa fa-vector-square)
            Sensors and routers and their position
            ::icon(fa fa-thermometer-half)
            Position of traps
            ::icon(fa fa-cat)

Traps

mindmap
    Trap
    ::icon(fa fa-cat)
        Position according to plan
        ::icon(fa fa-map-marked-alt)
        Position within the collection hierarchy
        ::icon(fa fa-database)
        Type of the trap
        ::icon(fa fa-newspaper)
        ID corresponding to trap
        ::icon(fa fa-barcode)
        Adhesive sheets
        ::icon(fa fa-border-none)
            ID for every adhesive sheet
            ::icon(fa fa-barcode)
        Collecting the data
        ::icon(fa fa-user)
            Mobile application
            ::icon(fa fa-mobile)
                Images of whole trap
                ::icon(fa fa-images)
                Images of single pests
                ::icon(fa fa-search)
                Images of previous samplings
                ::icon(fa fa-file-image)

Sensors

mindmap
    Sensor
    ::icon(fa fa-thermometer-half)
        Device collecting bluetooth signals of sensors
        ::icon(fa fa-microchip)
            LoRaWan sender forwarding the sensor data
            ::icon(fa fa-broadcast-tower)
                Receiver collecting data and storing data in a timeseries database
                ::icon(fa fa-wifi)
                    Application transferring data from timeseries databases in central database
                    ::icon(fa fa-database)

Report

Reports provide a summary of all IPM related data in a certain time range

mindmap
    Report
    ::icon(fa fa-list)
        Development over time
        ::icon(fa fa-chart-bar)
            Sensor data: Temperature, Humidity, ...
            ::icon(fa fa-thermometer-half)
            Pests
            ::icon(fa fa-bug)
        People involved in administration and in collecting the data
        ::icon(fa fa-users)
        Floor plan including locations of traps and sensors
        ::icon(fa fa-map)
        Treatments of the collection
        ::icon(fa fa-broom)

Integrated Pest Managment

Recording pests

To insert a new recording or edit an existing one, click in the correspondig cell of the table. A window as shown below will open where you can enter the number of observed pests, their state (provided the state is present) and any notes.

Subsections of Integrated Pest Managment

Integrated Pest Managment

Bycatch

Along with the pests you may find organisms that are no threat for the collection but should be monitored anyway. To include these organisms, click on the Bycatch button in the IPM form or choose Administration - Collection tasks - IPM - Taxa, Settings from the menu. A window will open where you can choose the organisms that should be recorded. See chapter Settings for details.

Integrated Pest Managment

Outside traps

ToDo

Ausarbeitung erst wenn Verwendung klar ist

To record pests on specimen, choose the in the display options. If the tab Pests on specimen is not shown in the IPM form, click on the Settings button to open the settings. See chapter Settings for details.

If pests are observed outside traps, e.g. in a room this can be documented in the Pests ouside traps tab. With the Add a collection where pests had been detected button you can add the corresponding part of your collection. A table column for the selected collection will be inserted and you can enter your data. With the Details button you can inspect the details of the selected collection.

Integrated Pest Managment

Specimens

ToDo

Ausarbeitung erst wenn Verwendung klar ist

To record pests on specimen, choose the in the display options. If the tab Pests on specimen is not shown in the IPM form, click on the Settings button to open the settings. See chapter Settings for details.

If pests are observed on a specimen this can be documented in the Pests on specimem tab. With the Add a specimen where pests had been detected button you can add the corresponding specimen. A table column for the selected specimen will be inserted and you can enter your data. With the Details button you can inspect the details of the selected specimen.

Integrated Pest Managment

Specimen groups

ToDo

Ausarbeitung erst wenn Verwendung klar ist

If pests are found in groups of specimens like convolutes, fascicles etc. and you do not want to document this for every single specimen, you may use the option to document it for the fascicles etc. instead. If the tab Pests on groups of specimen is not shown in the IPM form, click on the Settings button to open the settings. See chapter Settings for details.

If pests are observed on a group of specimens this can be documented in the Pests on groups of specimem tab. With the Add a group of specimen where pests had been detected button you can add the corresponding groups of specimens. A table column for the selected group of specimen will be inserted and you can enter your data. With the Details button you can inspect the details of the selected group of specimens.

Integrated Pest Managment

Taxa

The IPM (Integrated Pest Managment) uses DiversityTaxonNames as a backbone for Taxa. By default the public available database DiversityTaxonNames_TaxaVaria on the server tnt.diversityworkbench.de is used as a source. If you want to build your own source, you have to follow the guidelines below to ensure the functionallity of the forms.

Resources  

Preview images  

The form for handling IPM data in DiversityCollection shows preview images for the objects like pests as shown below.

These preview images are retrieved from the corresponding lists in DiversityTaxonNames. To create these previews, choose a source, align it, remove the background and reduce the size to 50 (height) x 100 (width) pixel.

Insert the preview image as a resource (see above) with the Type preview (see below). The title of the image must correspond to the stage resp. remain as defined in the taxon list. If the preview image is taken from a foreign source you shoud enter the source, copyright etc. of image (see below).

Images  

The original image of the preview should be included as as second image with coresponding data but Type image (see below). These images will be shown if the user clicks on the preview image in the table. You may add additional images.

Resources  

Resources that should be shown when the user click on the link in the second column are added as shown below with the type information.

 

Group

The group shown in the interface is retrieved from the list entries with the IPM - group marker where the value defines the sequence for the corresponding groups. These are shown in the first column of the IPM form.

 

Common names 

The first common name for the organisms or higher taxa are used for display in the IPM form. Please provide one common name for every taxon.

 

Life stages, remains

The life stages and remains of a taxon defined in DiversityTaxonNames (see below).

To make them available in DiversityCollection they must be included in the corresponding list (see below).

 

Integrated Pest Managment

Settings

Taxa

To set the taxa shown in the form, click on the  settings button or choose Administration - Collection tasks - IPM - Taxa, Settings from the menu. As window as below will open. 

There are 3 lists:

  • Pests
  • Beneficials
  • Bycatch

Select the taxa that should be shown in the main form. The taxa used for IPM are by default taken from the public database DiversityTaxonNames_TaxaVaria provided via tnt.diversityworkbench.de. If you want to set up your own list you can change the source. Click on the button to set the server and database, the button to set the project within your database and the buttons for every list to set the lists. 

Display options

In the tab Display options you can choose

  • If the scientific names should be shown in the interface
  • If the collections other then traps (e.g. rooms) should be available for recording of pests
  • If the specimens should be available for recording of pests
  • If the convolutes, fascicles etc. should be available for recording of pests

With the Reset taxa button you can requery the taxa from DiversityTaxonNames to get the latest lists.

Integrated Pest Managment

Traps

Traps consist of two parts. One part is defined in the collection management including the position of the trap. The second part is e.g. the adhesive foil for catching the pests. The existing traps are shown in the collection hierarchy (see below)

If you add e.g. a pest taxon to a trap and so far no second part (= e.g. the adhesive foil) exists, the program will ask you for adding this part and insert the taxon there.

Integrated Pest Managment

Treatments

If you apply a treatment in your collection, you can document the location etc. in the application. In the IPM-form select the tab for the Treatment.

In the collection hierarchy select the part (e.g. a room) where the treatment has been applied. Next click on the add button to add a treatment. If so far no treatment has been defined, the program will ask you if one should be defined.

ToDo

Ausarbeitung erst wenn Verwendung klar ist

Integrated Pest Managment

Beneficials

ToDo

Ausarbeitung erst wenn Verwendung klar ist

If you apply an beneficial organism in your collection, you can document the taxon, source, location etc. in the application. In the IPM-form select the tab for the Beneficials.

In the collection hierarchy select the part (e.g. a room) where the beneficial organism has been applied. Next click on the add button to add a benefical. If so far no benefical has been defined, the program will ask you if one should be defined. See chapter Settings for details.

Integrated Pest Managment

Charts

ToDo

Ausarbeitung erst wenn Verwendung klar ist

To generate a chart e.g. for the pests frequence, select the part of the collection tree for which the chart should be created for. Then in the Chart tab click on the Generate chart button. A chart will be generated. To see the chart in a separate window, click on the Show chart button. With the Save button you can save the generated chart as a png image and with the Export button you can export the data corresponding to the chart as a text file. The Open directory will open the directory that contains the exported file.

In the Settings tab …

In the Metrics tab …

Integrated Pest Managment

Cleaning

ToDo

Ausarbeitung erst wenn Verwendung klar ist

If you apply a cleaning in your collection, you can document the location etc. in the application. In the IPM-form select the tab for the Cleaning.

In the collection hierarchy select the part (e.g. a room) where the cleaning has been applied. Next click on the add button to add a cleaning. If so far no cleaning has been defined, the program will ask you if one should be defined.

Integrated Pest Managment

Collections

If no top collection is set, the program will ask you to select a top collection. You can change the top collection with the button at the top showing the top collection or as described below.

The Collection tree at the left part shows an overview of the current collection. The top collection can be set by the user. Choose a collection in the tree you want to set as starting point. A button will appear above the tree, e.g. Set room …. After setting a new starting point all data will be restricted to the selected collection and its inferior objects. To return to a superior collection, click on the Change to parent collection button.

 

Integrated Pest Managment

Dates

Inspection dates

The Inspections show the previous dates for inspections of the traps. The current date will be added at the end of the list. If you want to add a date that is missing in the list, click on the button. You may restrict the range of the dates with a click on the button. A window as shown below will open, where you can set the upper and / or lower border of the range.

The lower and/or upper border will then be shown underneath the list for the dates (see below).

To edit a border, just click on it and edit the value in the window that will open. To remove a border use the button.

Integrated Pest Managment

Images

ToDo

Ausarbeitung erst wenn Verwendung klar ist

Integrated Pest Managment

Plans

ToDo

Ausarbeitung erst wenn Verwendung klar ist

You can provide floor plans for your collection and pinpoint the locations or your sensors and traps.

Integrated Pest Managment

Report

ToDo

Ausarbeitung erst wenn Verwendung klar ist

Reports can be created in the Report tab.

The collection hierarchy selects the part (e.g. a room) for which the report will be created. You can choose the time range for the report. If no Schema is selected plain xml will be generated. With the open file button choose a schema applied for the report. There are several schemas provided by the software, but you can create some of you own. You can include charts for either locations or rooms and plans of your collection.

To create the report, click on the create report button. To print it, use the button.

Integrated Pest Managment

Sensor data

Prometheus

Installation of Prometheus

To install a Prometheus follow the guidlines provided no the homepage. server choose   from the menu.

Configuration of Prometheus

To configure a Prometheus server choose from the menu.

Starting of Prometheus

To configure a Prometheus server choose from the menu.

 

Naming conventions for Prometheus nodes

The nodes/sensors on the prometheus should be named according to the follwoing convention: [Domain]_[MAC]_[Type]_[Units].

  • Domain:    e.g. IPM
  • MAC:    MAC of the sensor written without the :  and in lower case e.g. 00a49484b3f0 for 00:A4:94:84:B3:F0
  • Type:    The type of the sensor, e.g. temperature, battery, humidity
  • Units:    The measurement units of the metric, e.g. celsius, ratio

some examples:
IPM_3453a5f60087_battery_ratio
IPM_3453a5f60087_humidity_ratio
IPM_3453a5f60087_temperature_celsius

An examplethe o configure a Prometheus server choose from the menu.