E-Ecology Documentation and Guidance

Last updated: February 2018, Stacy Shinneman

The e-Ecology Virtual Laboratories represent a collaborative effort between the University of Amsterdam Institute for Biodiversity and Ecosystem Dynamics and SURF Computing to manage bird tracking data and develop tools for data exploration, analysis and visualization. This wiki is designed to facilitate access to the data and tools within the Virtual Laboratories and to provide a forum for collaboration.

The e-Ecology database contains many different datasets, each of which is contained within its own schema. Prior to 2018, the e-Ecology database was also referred to as the FlySafe database.

UvA-BiTS Data

Bird data collected with the UvA-BiTS Bird Tracking System is managed within the gps schema of the e-Ecology database.

Note: We are continually working on improving UvA-BiTS services, including data processing and Virtual Lab functionality. In some cases, this has enabled us to extract more information from old GPS log files which is then incorporated into the database. These changes may result in slight differences when you reprocess historic data.

• e-Ecology UvA-BiTS database for general use (views)
• e-Ecology UvA-BiTS tables behind the views (not accessible for normal use)
• How to access the e-Ecology database
• Reference systems for GPS coordinates and altitudes
• Useful Queries

UvA-BiTS Services

• Visualization Tools

UvA-BiTS KMZ Generator:

Produces kmz files of UvA-BiTS bird tracking data to be viewed in Google Earth.

Tracker Calendar:

Calendar overview with daily statistics of GPS-tracker

Flight Generator:

This tool produces GPX files from UvA-BiTS tracking data for dynamic Doarama visualizations.

BirdView:

This service is currently not available. Access meterological and radar data and overlay with GPS bird tracking data.

BirdSim:

This service is currently not available. More dynamic version of BirdView that allows the user to scroll through weather data in time and space.

• Dashboard: These web pages allow UvA-BiTS users to get an overview of the raw data files of GPS bird tracking devices they have access to and to access the dashboard for administering projects.

• Annotation tables for uploading GPS annotation data into your own schema and sharing your tables with other users. This service is currently not available.
• SMS tables for storage of SMS messages send by trackers.
• CartoDB usage and limitation of CartoDB server

Changes to the UvA-BiTS data model in 2014

Important In the summer of 2014 we have re-arranged the administrative part of UvA-BiTS (and e-Ecology) in the database. End users may have to adapt their programs the following way:

• The uva_*_limited views that used to exist in the gps schema are gone. Most of them should have been replaced with an equivalent ee_*_limited counterpart.
• The new ee_*_limited views show a superset of the same information as before, but enhanced with new project information.
• Some column names in the ee_*_limited views may differ from the previous views.
• There are new limited views:
  • gps.ee_project_limited: shows your projects' information
  • gps.ee_shared_*_limited: set of data you are able to see related to trackers that a project is sharing with a project you belong to
• Special attention: gps.uva_device_limited is now replaced by gps.ee_tracker_limited. For each tracker, you now see which project provides you access to that tracker.
• Also, gps.uva_tracking_limited is gone. Instead of that we have gps.ee_tracker_speed_limited, which adds speed columns to the original data. This amounts to a merger of gps.ee_tracking_limited, gps.ee_tracking_speed_3d_limited and gps.ee_tracking_speed_limited.
• UvA-BiTS Data Model - OLD

Other e-Ecology Datasets

ENVIRONMENTAL DATA

• Elevation Data
• Weather Forecast Data (ECMWF) Restricted to FlySafe users.

FLYSAFE

Data related to European Space Agency FlySafe project. Financed by the Royal Netherlands Air Force.

• Argos GPS Data Model
• Radar Data Model
• Wind Profile Data Model
• How to access the e-Ecology database

Other e-Ecology Services

e-Ecology GPS Bird Track Generator: Produce kmz files of ARGOS/GPS bird tracking data from the FlySafe project to be viewed in Google Earth.

Administration: Information about user rights and data processing tasks.

Bookkeeping: Description of tables related to e-Ecology data processing and archiving.

ToDo