Partnership for Observation of the Global OCeans
Plymouth Marine Laboratory
Prospect Place
Plymouth, PL1 3DH, UK
A mobile app for identifying plankton and crowdsourcing data on species distribution
in the
GEOSS Architecture Implementation Pilot – Phase 7
(AIP-7)
Response Due Date: 7 April 2014
Programmatic/Technical POC:
Alex Kraberg
Email: Alexandra.Kraberg@awi.de
Phone: +49 4725 8193236
Programmatic POC (POGO Secretariat):
Sophie Seeyave
Email: ssve@pml.ac.uk
Phone : +44 1752 633424
Due Date: 7 April 2014
GEOSS AIP-7 CFP Response
POGO Response to the GEOSS AIP-7 CFP

Overview
In a world of rapid climate change and ecological degradation in many parts of the world
it is more important than ever to be able to monitor biological changes and their
ecological implications. However, the required taxonomic/ecological expertise is rapidly
declining, while the need for monitoring the biological environment and therefore
identifying relevant species remains. As the training of dedicated taxonomists requires
many years, these monitoring efforts will increasingly be in the hand of nontaxonomically trained analysts. These will need comprehensive and standardized
information to enable them to produce equally standardized high quality biodiversity
assessments with detailed information that, ideally, does not require taxonomic expertise.
Traditionally the process of identification of an organism required extensive literature
resources in addition to taxonomic expertise, thus making reliable identification
extremely challenging for most analysts.
Mobile technology can help to address some of these problems since it can enhance the
access to background material and facilitate more efficient communication between the
users of these resources. Apps can also greatly accelerate the process of data acquisition.
Some mobile applications already work with images, but they try to use representative
‘pretty images’ and rarely the opportunity to compare IDs from different regions. Some
of these apps provide facilities to upload images to a common data pool (e.g. Project
Noah, http://www.projectnoah.org/organisms) but no means to immediately identify them
other than by browsing through the data sets on the basis of some prior knowledge as to
the identity of the taxon. None of the available apps yet provide a combination of
observation, identification keys and access to background data either on- or offline. In
particular, none provide keys that facilitate identification or at least a ‘narrowing down’
to major groups, by using non-taxonomic identification characteristics. Standard
dichotomous keys depend on the user being able to identify morphological characteristics
in a certain sequence. If some of these cannot be seen then the user cannot proceed. In a
matrix key the user can select relevant characteristics, matching the organism under
investigation, in any order – with an algorithm calculating the likelihood of having
selected organism x, y or z. Examples are LUCIS or ETI keys (http://lucidcentral.org,
http://www.eti.uva.nl/about/). The latter also publishes contributed keys online.
Apps are already playing a considerable role in the development of citizen science in
support of environmental monitoring projects (e.g. monitoring for harmful algal blooms,
http://fulcrumapp.com/apps/harmful-algae-bloom-survey/) but could be of even greater
value if they did not only facilitate easy, jargon-free reporting of incidents, but contained
a science education component making the reported data more accurate.

Proposed Contributions
 Key application support
We propose an app that provides interactive identification aids (based on non-taxonomic
as well as taxonomic characteristics) for different plankton groups together with fact
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Due Date: 7 April 2014
GEOSS AIP-7 CFP Response
sheets for these groups and the opportunity to compare IDs to images of that taxon for
many different areas. The app will therefore source biogeographic records from the
PLANKTON*NET database and other partners (e.g. SAHFOS and other POGO
members) to provide biogeographic background information to check the likelihood of
observing species x in area a or b.
The PLANKTON*NET app will use a dual approach for the identification of specimens
in the field or lab in situations where extensive expert literature is not available or cannot
easily be obtained e.g. by field station or universities in developing countries.
Identification aids will be delivered in the form of matrix keys that allow the user to
select characteristics of the organisms and the key calculating the probability of a certain
species having been seen on the basis of character combinations entered for the species
(Figure 1).
Figure 1: Components of the proposed PLANKTON*NET app. (ESKP= Earth system
knowledge platform). ESKP can be used as a forum for dissemination
At the same time, the app will also provide a facility for uploading data into a special
collection on the PLANKTON*NET site (http://planktonnet.awi.de). This will in time
further increase biogeographic coverage, thereby initself aiding later identifications for an
organism in a given area, but only after a review period to ensure that the uploaded
material adheres to the same quality standards and formatting conventions as the
underlying taxonomic database system(s). The organism images to be uploaded can be
identified prior to the upload on the basis of the matrix keys and additional material, such
as literature sources that will be made available on- and offline. Together with the actual
taxon record the user will also be able to record environmental data from their sampling
site, e.g temperature, salinity, water colour or general weather comments (sunny, overcast
etc.)
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The app should automatically deliver metadata on the geographic position of image
recording that should be as close as possible to the sampling point. Personal data is
required for managing point-to-point user interactions and to prevent the infrastructure
from misuse. This will involve a certain degree of access control to avoid spam.
Target audience: 1. Non- specialized plankton analysts that carry out ‘as far as you get’
IDs using all available resources in the PLANKTON*NET app., 2. Scientists needing
background information in a field situation where the necessary material might not be
accessible
Implementation
The implementation will have to involve two parallel steps:
1: Design of the actual matrix key: The matrix key, once set up, will be flexible in that
at a low taxonomic resolution it can be used to distinguish between very broad groups.
This can be extended to many different types of taxon groups by designing hierarchic sub
keys. Crucially this key will be based on information that is not strictly taxonomic in
nature (e.g. size ranges, colours, habitat, symmetry) and therefore can reliably be
provided by non-experts.
This will be more extensive process and we here propose an initial prototype for centric
diatoms. This will facilitate a global utility of the app, since centric diatoms comprise
some of the most common diatom taxa in the world. The app will require an offline
component as well so that a minimum functionality is also available when internet access
is not available. Importantly once designed the keys can easily be extended to additional
taxon groups including benthic or even terrestrial ones.
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GEOSS AIP-7 CFP Response
Figure 2: Work flow for identifying organisms using the PLANKTON*NET app.
Starting with an unidentified image, the user will enter a combination of simple
information into a general key. If a broad organismal group can be identified from this
the user can then attempt to proceed to more detailed keys, if a group cannot be
identified, further background information might be consulted based on very basic
information available, to help facilitate a better description of general characteristics, and
later identification of the organism using taxonomic keys.
2. Data assimilation and data preparation to be queried by the matrix key in the
app:
To populate the matrix key within the app it will be necessary to extend the database
structure of the PLANKTON*NET database with additional fields holding the
information that can be chosen from the key. Examples include, size, shape and colour,
plus further fields for entering image metadata, which will facilitate annotation (and later
selection) of images on the basis of characteristics such as orientation of the cell in the
image. These fields will form the basis of the matrix key, while the purely taxonomic
information will be used to populate species/species group pages forming the end point of
the identification process after moving through the key. The latter can also be an element
that can be made available offline.
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Societal benefits
The app would support the following GEO Societal Benefit Areas: Agriculture, Health,
Biodiversity, Water and Ecosystems. It would be very useful to a wide range of users,
from scientists to coastal resource managers and fish/shellfish farmers. Specifically, it
would enable non-specialists to detect and report the (likely) presence of Harmful Algal
Bloom species, some of which can be extremely detrimental at low concentrations
(therefore not detectable visually as “red tides” that discolour the water). The app would
be particularly beneficial for developing countries, where traditional taxonomic resources
and training are scarce, but mobile (smart)phones are commonplace. The app would also
enhance the global coverage of plankton data and the detection of species introduced to
new areas via ballast water. Global analyses of these data could be undertaken in
collaboration with the Global Alliance of Continuous Plankton Recorder Surveys
(GACS), an international programme led by the Sir Alister Hardy Foundation for Ocean
Science.
Links to other areas of GEO
The proposed app addresses the Target Area “Environmental Monitoring using Mobile
Sensors, Citizen Observatories; Crowd Sourcing” as defined in the CFP. Although this
proposal focusses on plankton identification, the principles and software could be applied
to the identification of any marine, freshwater or terrestrial species. In addition to the
obvious links across the Blue Planet Task, the proposal would be relevant to the
GEOBON community.
 Architecture and Interoperability Arrangement Development
The PLANKTON*NET database uses the Darwin core metadata standard to be able to
handle taxonomic, collection and biogeographic data but the data model is flexible and
can easily be extended. All PLANKTON*NET data are published under a Creative
Commons Licence. The database is also configured to use the Biocase software to
connect it to different information networks such as the Global Biodiversity Information
Facility, GBIF (linking PLANKTON*NET to GBIF is already planned for 2014) and
other information networks for biological data. Prototype links to the PANGAEA data
system (http://pangaea.de) also already exist thus providing links between the biological
and accompanying physico-chemical data and importantly also the regular use of imagebased records as standardized metadata for numerical data such as biological timeseries.

Description of Organizations
The Partnership for Observation of the Global Oceans (POGO) is an international
network of oceanographic institutions that promotes global oceanography, in particular
sustained, long-term ocean-observing systems; shared use of infrastructure, data and
information; capacity building; and public outreach. POGO has 39 members from 21
countries; members are typically oceanographic research institutions, represented at the
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GEOSS AIP-7 CFP Response
Director level. POGO has been a supporter of GEO since its inception, and is a
Participating Organisation in GEO. POGO led the development of the “Oceans and
Society: Blue Planet” Task (SB-01), which brings together all the ocean observing
elements within GEO under a single umbrella.
The work described in this proposal will be undertaken by POGO members, with support
from the POGO Secretariat, which will act as the liaison between its members and the
GEO Secretariat / OGC. Different POGO members may provide different in-kind
contributions, such as data, programming or guidance for the application’s design.
Overall co-ordination will rest with the Alfred-Wegener Institute. The institute is located
in Bremerhaven with stations carrying out field and laboratory-based studies on the
islands of Helgoland and Sylt as well as in the city of Potsdam. The institute holds large
datasets on diversity, which are also archived in the Pangaea database and harvested by
GEOSS, MaNIDA and other data systems. AWI also operates different biodiversity
databases such as the Hustedt diatom database and the PLANKTON*NET database. The
latter is a collection of global taxonomic and biogeographic image-based data on phytoand zooplankton that has been online for 10 years. It now contains 11000 images of
phytoplankton, thousands of geo-referenced distributional records and additional
information such as an extensive reference collection and taxon detail pages with
summaries of all information in the database for a given taxon. Numerical data in
Pangaea can also be accessed. The database will serve as the initial source of all Apprelated information during the design of the prototype application and be modified as
necessary. PLANKTON*NET is supported by the general database support team in the
computing department of the Alfred-Wegener Institute.
The institute also has very extensive computing facilities and expertise and is involved in
many public outreach projects such as the project Earth System Knowledge Platform,
which aims to disseminate climate change-relevant information to different stakeholders.
Additional support through this initiative is sought for the development of the app.
But at present manpower can be devoted to the development mainly on the content
generation and content management side.
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Due Date: 7 April 2014
GEOSS AIP-7 CFP Response
Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research
Programmatic Contact
Alexandra Kraberg
Tel. + 49 4725 8193236
E-mail Alexandra.Kraberg@awi.de
Technical Contact
Stephan Frickenhaus
Tel. +49 471 48311779
E-Mail: Stephan.Frickenhaus@awi.de
Sir Alister Hardy Foundation for Ocean Science
Programmatic Contact
Prof Nicholas Owens
Tel: +44 (0)1752 633281
E-mail: njpo@sahfos.ac.uk
Technical Contact
Tanya Jonas
Tel: +44 (0)1752 633131
E-mail: tjo@sahfos.ac.uk
POGO Secretariat
Programmatic Contact
Sophie Seeyave
Tel. +44 (0)1752 633424
E-mail ssve@pml.ac.uk
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