EnviroInfo 2012: EnviroInfo Dessau 2012, Part 1: Core Application Areas
Copyright 2012 Shaker Verlag Aachen, ISBN: 978-3-8440-1248-4
“Finding Nemo” – Assessment and Visualisation of Biodiversity
Data in a Web-based Atlas
Konstanze Steinhausen1, Martin Winkler2, Carl-Heinz Genzel3, Heide-Rose Vatterrott4,
Heiko Brunken5
Abstract
What is the current distribution of the salmon? Has the population of the European otter declined? Which alien
species have most recently been discovered in Germany? The Biodiversity Atlas gives the answers. Since 2006, the
Project Group AG Biodiversity has been developing the Atlas at the Bremen University of Applied Sciences in
cooperation between the Fish Ecology Lab and the Institute of Informatics and Automation (IIA). What started as a
rudimentary cartography service for fishes of Germany and Austria has evolved to a comprehensive web-based tool
for assessing and communicating biodiversity data. Today it is used in several projects to map species distribution
and to depict specific biological information, e. g. about amphibians in Pernambuco (Brazil) or mammals in the city
of Bremen (Germany). The information is gathered through expert networks, literature or public authorities. The aim
is to offer a scientifically sophisticated instrument to display highly topical data to the interested public in an
aggregated and easily understandable manner. By this means the Biodiversity Atlas provides a solution for the
sustainable protection of species and habitats.
1.
Introduction
Despite the efforts of many countries to protect and preserve endangered species the numbers of species
worldwide, and also in Germany, decline dramatically. The IUCN report of 2009 (IUCN 2010) reveals
that approximately 17,000 of a total of 47,000 assessed species are threatened with extinction. Among
these are 21% of all known mammals, 37% of all known freshwater fishes or 70% of all known plants.
43% of all German native vertebrates recently were classified as extinct, endangered or extremely rare
(Pauly/Ludwig/Haupt/Gruttke 2009). Scientists estimate that the current rate of extinction exceeds the
natural extinction rate by the factor of 100 to 1000. Most extinction is considered to be human-caused. In a
survey among biologists in 1998 (American Museum of Natural History 1998) a majority of 70%
predicted that one-fifth of all species alive today will become extinct in the next 30 years, and over 30%
think that as many as half of all species will have disappeared. The observed mass extinction is considered
to be at least equally dangerous for the future of mankind as the climate change. The community of
nations has realised this threat and is trying to find solutions to stop species loss. Therefore, the UN
declared the years 2011 to 2020 as the United Nations Decade on Biodiversity. One of the strategic
objectives for this decade is to promote public awareness for biodiversity issues and to sensitize for the
need to protect species. The scientific community is requested to create indicators and data, but also
1
2
3
4
5
Hochschule Bremen, [email protected]
Hochschule Bremen, [email protected], Schwachhauser Ring 55, 28213 Bremen,
[email protected]
Hochschule Bremen, Fakultät 4 Elektrotechnik und Informatik, Flughafenallee 10, 28199 Bremen,
[email protected]
Hochschule Bremen, Fakultät 5 Natur und Technik, Internationaler Studiengang Technische und Angewandte Biologie,
Neustadtswall 30, 28199 Bremen, [email protected]
communicate science platforms for innovation in biodiversity research and to find opportunities to expand
science communication on biodiversity. An essential prerequisite for a sustainable protection is to gather
precise information about the biology and distribution of species. The Biodiversity Information Standards
group recently has found 675 biodiversity information projects worldwide (TDWG 2012), but still there is
a big need for easy-to-use digital tools linking biodiversity data with nature mapping features for building
up regional biodiversity databases.
Regarding the process of gathering and
communicating faunistic and floristic data
in Germany there are currently two
divergent trends visible. According to
legislative
guidelines
(EU
Water
Framework Directive, Habitats Directive)
certain groups of species and selected
regions have been examined and assessed
professionally by public offices, and the
results have been directly reported to the EU
authorities via GIS based systems.
Additionally, research and educational
institutes tend to concentrate on highly
specific topics and publish their results in
specialized magazines today. But classical
monographs of species or species groups, or
qualified reports about specific regions are
published more rarely. As a consequence
the current situation seems ironic: Despite
the general awareness on the need for
collecting and assessing biodiversity data
Figure 1
and increased governmental efforts, a major
Distribution map and species information of Rhinella
deficiency in the collection and updating of
crucifer (WIED-NEUWIED, 1821), Atlas da Herpetofauna
faunistic and floral distribution data is
do Estado de Pernambuco
prevailing. In this circumstance, the
(Moura/Santos/Brunken 2012)
enhanced involvement of the voluntary
element (re)gains an increasing importance.
In order to support this ambitions the development of an easy to use and scientifically sophisticated
instrument, which enables a professional collaboration and coordination on topics concerning species and
environment protection is one major prerequisite. This concern was the main impetus for the development
of the Biodiversity Atlas.
2.
The Biodiversity Atlas
The Biodiversity Atlas offers a tool-set to collect and manage biodiversity data and to display species
distribution maps as well as additional species related information, e.g. systematics, species biology,
habitat demands, conservation status and more (fig. 1).
Today, with the technological resources and online tools of Web 2.0 a simple and easy-to-use
participation through associations and environmental enthusiasts can be accomplished, while, at the same
Copyright 2012 Shaker Verlag Aachen, ISBN: 978-3-8440-1248-4
time, the digital recording and the uniform data structure provides a high degree of data quality. Combined
data sets from smaller, local studies contribute to a highly topical and scientifically valuable data basis,
from which in turn new questions about environmental and species protection can be derived. The
Biodiversity Atlas is not intended to compete with other online species distribution databases. It rather
tries to fill the gap that exists between global (e. g. AmphibiaWeb 2012; Fishbase: Froese/Pauly 2012) and
local (e. g. land registry databases) data set resolutions.
This project would also like to support and contribute to the Open Data initiative. Data, which is
otherwise hard to obtain or unavailable to the interested general public can be presented in an aggregated
and easily understandable manner. Data privacy aspects play an important role when publishing data.
Every author has full control about his data, and can decide how open the access should be.
Furthermore the service is developed under the resolution of using solely free available licenses. This is
due to the fact that the service should be deployed worldwide. Furthermore it can benefit from the
knowledge of the Open Source developer community.
Figure 2
Architectural infrastructure of the Biodiversity Atlas system
The Biodiversity Atlas is separated in several parts that offer different opportunities for using the system.
Therefore users are divided into four groups. Each has particular access rights. In this way the Atlas
directs to a variety of users with different intentions and knowledge. The first two user groups - guest and
registered - define the access to the front end of the content management system. They are authorized on a
low level. Guests can see the evidences of the species as well as information about a particular species.
They have simple reading access. In contrast to guests registered users have a user account for additionally
Copyright 2012 Shaker Verlag Aachen, ISBN: 978-3-8440-1248-4
recording evidences of species. Reported biodiversity data is visualized in the front end for public not until
the validation of the editorial staff. This is handled over the back end by two groups of administrative
personnel - manager and administrator - who check the records and manage the system.
Two essential technologies form the system. On the one hand the content management system Joomla!
(Version 1.5) supplies the user interfaces for getting access to the information as well as the data itself. It
is released under the GNU General Public License. On the other hand the geographical aspect of the Atlas
is implemented with geographic information systems. The maps are realized with the JavaScript library
OpenLayers and OpenStreetMap. In combination with Proj4js for transforming between different
geographic reference systems, it is possible to capture the biodiversity data together with its geographical
location as well as visualize it.
As seen in figure 2 the system uses different servers and offers several clients for the users. The above
mentioned technologies build a 3-tier-architecture that consists of a browser client that is connected to the
Joomla! server and to the web server of OpenStreetMap over the internet. Both are connected to their
particular databases.
3.
The Joomla! Biodiversity Atlas component
The full amount of data administration will be realized by administrative users in the Biodiversity Atlas
component in the backend consisting of 10 subject-specific tables (= managers) (fig. 3). The Species
Manager is organizing all species-specific information, e.g. scientific and common names, first author and
year of description, including preferences for displaying correct scientific names in the front end (in
particular setting first author’s name in brackets or not). In addition the Species Manager provides
WYSIWYG text editors for compiling species descriptions and commentaries and is organizing the
preview image.
The Location Manager is executing all information of locations where the specimens had been
registered. Locations can be determined by using given coordinates or by interactively choosing from a
manager integrated preview map. All coordinates will be transformed into the WGS84 reference system.
Locations can be either defined as an accurate point of observation or as a geometric centre of a given area
(e.g. national park) when no more information is disposable. The chosen option is reflected by a distinct
symbology of distribution points within the maps.
The primary task of the Measurement Manager is to combine a location with a specific date of a
sighting in which the day is the given maximum chronological resolution. The default option is to adopt
the geographical coordinates from the Location Manager. Besides from this additional coordinates can be
defined, for instance to distinguish a certain micro habitat in the field.
The last step in converting a faunistic field observation into a data set of the Biodiversity Atlas is to
define a specific record using the Record Manager by a combination of a measurement (which already
includes location and date) and a given species. In this process it is possible to mark a sighting as
concealed, so its accurate coordinate would not be publicly accessible on the species distribution map.
This is often required for not divulging the precise location of threatened or sensitive species. Instead of
this the Atlas will display the centre coordinate of a grid cell which intersects with the location’s
coordinate. The records can be tagged by additional attributes like record quality or type of sighting. The
attribute list can be amplified and individualized by using the Basics Manager.
Personal information of the administrative personnel is administrated by the Editor Manager,
predominantly serving as an internal control and information tool.
Copyright 2012 Shaker Verlag Aachen, ISBN: 978-3-8440-1248-4
The Layers Manager facilitates the depiction of several map sources. In addition to OSM layers others
can be used like GIS shapes or layers from other map servers (e.g. Google Maps). The Areas Manager
enables the administration of atlas-specific areas of interest when opening the distribution maps as a
default setting.
Due to ongoing rearrangements in biological systematics there is no fixed taxonomic hierarchy (e.g.
class, order, family, genus) of given species or species groups. Because of this the implementation of a
flexible Taxonomy Manager is one of the most important features within the Biodiversity Atlas to
guarantee a long-term data management.
Information about the status in a Red Data Book of threatened species is an important trait for nature
conservation purposes. The Red List Manager makes allowance to the fact that one species can be
registered with different Red List classifications for different areas (e.g. local, regional, global) and that
this status can be changed over the years.
Figure 3
The Biodiversity Atlas component (highlighted with green frame) is comprising 10 subject-specific tables
(= managers) for detailed content administration
Source: Moura/Santos/Brunken 2012
4.
Mobile Application
Besides these components, there is a mobile client and a third server. Those components are in
development to extend the basic system for improving the actuality of the data and for raising the grade of
traceability. The client is a mobile application for Android smartphones. It provides the notifying of a
record directly after its sighting outdoors via a mobile device. This enables registered users to report a
record as fast as possible. That is also supported with the determination of the position via the GPS
positioning function of the smartphone. The traceability of a record is raised with the capturing and
sending of pictures that is a unique feature of the mobile application.
As distinguished from the PHP-based logic of the Joomla! server, the data is sent in a raw format and
inserted in the database via the additional server.
Copyright 2012 Shaker Verlag Aachen, ISBN: 978-3-8440-1248-4
5.
Forecast
For the future development of the Atlas it is planned to implement data interfaces to connect to existing
local databases. This will enable the system to import large sets of data which have already been digitally
stored but not been published as species distribution maps. An additional advantage is the possibility to
combine available scientific data of other internet-based platforms through data interfaces. The derived
synergistic effects of such interlink are of great value concerning questionings of species and
environmental protection.
Furthermore the implementation of a simple GIS functionality into the Biodiversity Atlas will offer
visitors to run spatio-temporal queries to get a quick picture of regional or seasonal species distribution.
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Copyright 2012 Shaker Verlag Aachen, ISBN: 978-3-8440-1248-4