Research Ideas and Outcomes : Workshop Report
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Corresponding author: Mareike Petersen (mareike.petersen@mfn.berlin)
Received: 30 Jan 2019 | Published: 31 Jan 2019
© 2019 Mareike Petersen, Falko Glöckler, Jana Hoffmann
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation: Petersen M, Glöckler F, Hoffmann J (2019) Harmonizing plot data with collection data. Research Ideas and Outcomes 5: e33509. https://doi.org/10.3897/rio.5.e33509
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Although plot or monitoring data are quite often associated with objects collected in the plot and stored in specific collections, controlled vocabularies currently available do not cover both disciplines. This situation limits the possibility to publish common data sets and consequently brings a loss of significant information by combining plot-based research with collection object associated data. To facilitate the exchange and publication of these important data sets, experts in natural history collection data, ecological research, and environmental science met for a one-day workshop in Berlin. The participants discussed data standards and ontologies relevant for each discipline and collected requirements for a first application schema covering terms important for both, collection object related data and plot-based research.
application schema, biodiversity, data standard, ecology, monitoring, natural history collection
30 May 2018, Museum für Naturkunde Berlin
Plot sampling is a widely used method in ecology and biodiversity research. These inventories are commonly accompanied with the collection of voucher specimen for e.g. further identification or analysis. Whereas gathered information of plot observations are usually assigned to a plot or a plot observation to a particular time, specimen in natural history collections are managed on unit level with all information and measurements attached to a specimen. Currently there is a variety of controlled vocabularies (thesaurus) available for biological and related disciplines. A set of defined descriptive terms are either arranged in structured data standards or put in relation to each other in an ontology. However, controlled vocabularies designed for a standardized exchange of collection data, e.g. Access to Biological Collection Data (ABCD,
Within the scope of the research and service project “ABCD 3.0 – A community platform for the development and documentation of the ABCD standard for natural history collections” *
The workshop was carried out in the framework of the ABCD 3.0 project, a colloboration of the Museum für Naturkunde Berlin and the Botanical Garden and Botanical Museum Berlin Dahlem. During the workshop experts of natural history collections, biodiversity standards and ecological/environmental science met in order to share their experience and collect their requirements for the publication of plot-based data. The participants examined different domain-specific vocabularies and discussed terms necessary to describe plot-based research data including e.g. habitat characterization, time series, monitoring, and the collection of sample specimen. The workshop's results are presented in this report. Furthermore necessary tasks towards an application schema for plot data were discussed and are documented here.
The workshop intended to evaluate whether the standard ABCD fulfills all demands and whether other domain-specific controlled vocabularies contain appropriate, supplementary terms for the publication of plot-based data. The aim for the one-day meeting was a first version of an application schema linking collection objects with plot-based research.
The workshop program included a short informative and an extensive interactive part (see Suppl. material
It was shown, that plot-like data, e.g. DNA samples, can be expressed with ABCD and its extension GGBN (
Following this, participants were asked to compile thematic use cases for plot-based research. Eventually, it was agreed to collaboratively work on a single, more general use case: the mapping of a habitat or biotope including multiple visits (time series). In a closing discussion session all relevant concepts were collected, their relationships to each other were considered, and the cardinality of each concept was reasoned. Fig.
Concepts of a first version of an application schema for plot-based data in combination with collection objects. Given are concepts discussed during the workshop and which should be incorporated in an application schema (compare Fig.
Concept |
Description |
Cardinality |
plot research | ||
project metadata |
details on the framework of the plot research (project, institution, scope, etc.) |
n |
spatial concept |
describing and related to the location of the plot |
1 |
temporal concept |
describing an observation or measurement at the plot in time |
n |
measurement |
any measurement conducted during plot observations (vegetation, soil, temperature, etc.) |
n |
person |
people conducting the plot research |
n |
multimedia object |
any multimedia objects associated with the plot / a plot observation |
n |
publication |
any publication associated with the plot / a plot observation |
n |
collection object | ||
specimen |
specimen observed / gathered during a plot visit |
n |
taxonomy |
determination / taxonomic identity of the specimen |
1 |
measurement |
individual measurement of the specimen |
n |
multimedia object |
any multimedia objects associated with the plot / a plot observation |
n |
publication |
any publication associated with the plot / a plot observation |
n |
identifier |
persistent identifier for the collected specimen |
1 |
storing collection |
collection holding the specimen |
1 |
First version of an application schema for plot-based data. Shown is a list of terms, their relations, and partly their cardinality important for habitat and biotope mapping (status: 30 May 2018, end of the workshop). Given is the flipchart diagram created during the workshop (see Table
The core of this first version of a plot-based application schema consists of a spatial concept, a concept related to and describing the location. A temporal concept, e.g. describing one plot observation or a measurement at the plot to a specific moment in time, is closely related and repeatable. Multiple other properties such as associated media or other measurements and the performed method can be related to this concept. During each plot visit the observation and/or the gathering of specimen could occur and should be recordable. The specimens themselves are accompanied with information about their taxonomy, individual measurements etc. and, in case of collection, any identifier and further information about the storing collection. Due to time limitation, it was not discussed how these concepts could be related to the direct plot measurements. These relations and other relevant terms mentioned during the discussion (e.g. project metadata, associated publication, and person) need to be addressed subsequently.
According to the set of vocabularies investigated during the workshop Veg-X seems to be the most promising standard covering various information necessary for the discussed use cases. In order to have a deeper look into the standard, to evaluate the overlap of terms, and to assess the possibility to extend ABCD with terms derived from Veg-X a mapping between ABCD and Veg-X is required. ABCD allows the representation of plot and plot-like data to some extent, but its structure currently limits the usability and impedes the publication of proper plot data in important portals such as GBIF (https://www.gbif.org/). Due to new developements, ABCD is no longer fixed in its hierarchical and collection object centralized form. This will facilitate the link to other appropriate vocabularies and to draw application schema for different plot-based research questions. On the other hand, the maintainers of other data standards should prefere to re-use appropriate ABCD terms over creating new terms as soon as they are going to extend their schema towards collection objects. Thus the development of a real application schema for plot-based data should be done in collaboration. The list of terms collected in this workshop will however serve as a guideline for the publication of plot data in the meantime and later on in consensus with experience in plot-like examples (e.g. sample with environmental DNA) and knowledge using ABCD over the last years (
The workshop was supported by ABCD 3.0, a DFG project funded under the LIS infrastructure platform. We thank G. Dröge for her inspiring talk and all participants for their valuable contribution and constructive comments on an earlier version of the report. The publication of this article was funded by the Open Access Fund of the Leibniz Association.
ABCD 3.0: Funded by the German Research Foundation (Deutsche Forschungsgemeinschaft), Scientific Library Services and Information Systems; partners: Museum für Naturkunde Berlin (MfN) and Botanical Garden and Botanical Museum Berlin Dahlem (BGBM).