What is CRITTERBASE?

CRITTERBASE is a software system developed by AWI and HIFMB to assist researchers in managing sample-based biodiversity data. It is open source and consists of two components:

  • Collector's App (client, backend)
  • Web service (server, frontend)
Start Exploring

Download video file: normal quality (158 MB) (08.10.2021)
⚠ for internal use only - do not share this file ⚠
Collector's App

Data collectors use the Collector's App to check the quality of their data; and to convert it into CRITTERBASE, too. It is platform independent (macOS, Linux and Windows) and written in Python.

Work locally

The Collector's App does not depend on any server structure. You can bring your data into the correct format locally and work with it, absolutely securely. You maintain complete control over your data.

Web service

The CRITTERBASE Web service is hosted by the AWI Computing Centre and offers online access to publicly available data.

Data security

We store our research data securely on the GitLab service of the AWI Computing Centre. Any changes are logged, automatic backups are made regularly and any transport is SSL-encrypted directly via git client software like Sourcetree.

REST service

A direct machine-to-machine communication with the CRITTERBASE Web service is also possible through a REST interface to allow for software-based queries.

Cloud Computing

The CRITTERBASE Web service can also be accessed via the REST interface within the AWI JupyterHub or other instances of the AWI Marketplace, with all data and code remaining securely in one place in the AWI Computing Centre.

Quality control

All data is subjected to a rigorous quality control. This includes the initial reading in of the data as well as the checking of data that has already been imported.

Reporting

The Collector’s App can create useful reports and overviews regarding the overall quality of the CRITTERBASE. Especially with very large amounts of data, this is absolutely essential in order to guarantee high data quality. Particular emphasis was placed on user-friendly feedback.

WoRMS integration

The Collector's App can query taxon names directly from WoRMS. Thanks to advanced buffering technology, WoRMS queries can be carried out rapidly. CRITTERBASE is an official partner of WoRMS.

SQL

When the Collector's App builds a CRITTERBASE, it sets up a clean PostgreSQL database. Especially if you are working locally, this means you can make direct queries to your local CRITTERBASE via SQL. This can also be done in R and Python - keeping everything you need for analyses and modelling neatly in one place

Extendable

Due to the modular and generic architecture and the choice of an agile programming language, it is relatively easy to make adjustments to the entire CRITTERBASE system.

Open Source

The whole project is Open Source and uses Ubuntu Linux, Python, Qt for Education, OpenJDK, jQuery, Apache, PostgreSQL and PL/pgSQL.

CRITTERBASE is a team effort ...

Alfred-Wegener-Institut, Bremerhaven
Karen AlbersDeveloper (Web service), computer science
Jan BeermannProject member BENOSIS - data provider, biology - ecology
Thomas BreyMain lead of CRITTERBASE, core member, biology - ecology
Kerstin BeyerSupport with data collection, biology - ecology
Daniel DamaskeAdvisory on data management & digitization at Deutsche Allianz Meeresforschung
Jennifer DannheimProject leader BENOSIS, core member, biology - ecology
Stephan FrickenhausStrategic support in data science/publication enabling, computer science
Manuela GuskySupport in data collection, biology - ecology
Birgit GlückseligSupport with data collection, biology - ecology
Michael GünsterAWI GitLab support, computer science
Miriam HansenSupport in data entry in CRITTERBASE, biology - ecology
AWI HelpdeskHelping in countless IT problems
Kerstin JeroschEU project coordination CoastCarb
Paul KlossLead developer, core member, computer science
Gesche KrauseStrategic support in enabling stakeholder interaction, social science
Roland KoppeLead support of AWI Computing Centre, Lead developer (Web service, computer science)
Peter KonopatzkySupport in mapping and geo-referencing, computer science
Rebecca KonijnenbergProject member WEECOS - data collector & R-code provider, modelling
Casper KraanSupport for data entry in CRITTERBASE, biology - ecology
Joerg MatthesSupport in virtual machines
Petra MeyerAdministration
PANGAEA teamSupport for making data citable
Hendrik PehlkeProject member WEECOS - R-code provider, modelling
Dieter PiepenburgProject leader PANABIO, core member, biology - ecology
Stefan PinkernellSupport on AWI JupyterHub and AWI Marketplace, computer science
Katharina TeschkeProject leader WEECOS, core member, biology - ecology
Tawfik SabbaghDeveloper (Web service), computer science
Andreas WalterSupport in mapping and geo-referencing, computer science
Paul WachterSupport in data entry in CRITTERBASE, computer science
Alexa WredeProject member of upcoming CRITTERTRAITS & R-code contributor, biology - ecology

Bundesamt für Seeschifffahrt und Hydrographie, Hamburg
Anne ElsnerData-exchange cooperation between MARLIN and CRITTERBASE
Gregor v. HalemData-exchange cooperation between MARLIN and CRITTERBASE

Financial support
AWIAlfred-Wegener-Institut through ESKP (Earth System Knowledge Platform)
BMELBundesministerium für Ernährung und Landwirtschaft
BSHBundesamt für Seeschifffahrt und Hydrographie, Hamburg
DFGDeutsche Forschungsgemeinschaft through Nationale Forschungsdateninfrastruktur (NFDI-4biodiversity)
HIFMBHelmholtz Institut für Funktionelle Marine Biodiversität an der Universität von Oldenburg
acknowledgments in alphabetical order


LIVE DEMONSTRATION

Would you like a little demonstration of the CRITTERBASE backend?

  • Introduction into all relevant sub systems.
  • Everything is shown in real time.
  • Helps you get a good overview of the entire system.
  • Best enjoyed with a cup of coffee.
  • It takes a while ... :)
  • You may want to use the jumps marks below for navigation.

Download video file: normal quality (345 MB) hi-res quality (1.89 GB) (08.10.2021)
⚠ for internal use only - do not share this file ⚠

WEB SERVICE

The more data marine ecologist contribute to CRITTERBASE, the more useful it will become for all of us.

Take a look at some screenshots and images

RELEASE TRAILER

Our trailer for the release of the CRITTERBASE Web service. We got a long way to go:

  • 10 years data mining and preparation
  • 400,000 records (so far)
  • 4 years of software development
  • 130,000 lines of code (so far)


Download video file: normal quality (120 MB) (19.06.2021)
⚠ for internal use only - do not share this file ⚠

COLLECTOR'S APP

Get the latest version here.

⚠ Unfortunately, we currently have no capacity to respond to any user requests. We ask for your understanding. ⚠

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