Proceedings of TDWG 1: e20366
The CDM Applied: Unit-Derivation, from Field
Observations to DNA Sequences
Patrick Plitzner , Andreas Müller , Anton Güntsch , Walter G. Berendsohn , Andreas Kohlbecker ,
Norbert Kilian , Tilo Henning , Ben Stöver
‡ Botanic Garden and Botanical Museum, Freie Universität, Berlin, Germany
§ Universität Münster, Münster, Germany
Corresponding author: Patrick Plitzner (email@example.com), Andreas Müller (firstname.lastname@example.org), Anton
Güntsch (email@example.com), Norbert Kilian (firstname.lastname@example.org)
Received: 16 Aug 2017 | Published: 16 Aug 2017
Citation: Plitzner P, Müller A, Güntsch A, Berendsohn W, Kohlbecker A, Kilian N, Henning T, Stöver B (2017) The
CDM Applied: Unit-Derivation, from Field Observations to DNA Sequences. Proceedings of TDWG 1: e20366.
Specimens form the falsiﬁable evidence used in plant systematics. Derivatives of
specimens (including the specimen as the organism in the ﬁeld) such as tissue and DNA
samples play an increasing role in research. The EDIT Platform for Cybertaxonomy is a
specialist’s tool that allows to document and sustainably store all data that are used in the
taxonomic work process, from ﬁeld data to DNA sequences. The types of data stored can
be very heterogeneous consisting of specimens, images, text data, primary data ﬁles,
taxon assignments, etc.
The EDIT Platform organizes the linking between such data by using a generic data model
for representing the research process. Each step in the process is regarded as a derivation
step and generates a derivative of the previous step. This could be a ﬁeld unit having a
specimen as its derivative or a specimen having a tissue sample as its derivative. Each
derivation step also produces meta data storing who, when and how the derivation was
done. The Platform's Common Data Model (CDM) and the applications build on the CDM
library thus represent the ﬁrst comprehensive implementation of the largely theoretical
models developed in the late 1990ies (Berendsohn et al. 1999).
‡ ‡ ‡ ‡ ‡
‡ ‡ §
© Plitzner P et al. 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
In a pilot project research data about the genus Campanula (Kilian et al. 2015, FUB, BGBM
2012) was gathered and used to create a hierarchy of derivatives reaching from ﬁeld data
to DNA sequences. Additionally, the open source library for multiple sequence alignments
LibrAlign (Stöver and Müller 2015) was used to integrate an alignment editor into the EDIT
platform that allows to generate consensus sequences as derivatives of DNA sequences.
The persistent storage of each link in the derivation process and the degree of detail on
how the data and meta data are stored will speed up the research process, ease the
reproducibility of research results and enhance sustainability of collections.
EDIT Platform, Taxonomy, Specimen
For funding of the EDIT Platform for Cybertaxonomy please refer to the presentation by
Kohlbecker & al. The Campanula project was funded by the German Research Foundation
(DFG, Deutsche Forschungsgemeinschaft) within the Scientiﬁc Library Services and
Information Systems programme (KI 1175/1-1, MU 2875/3-1).
Botanic Garden and Botanical Museum Berlin, Freie Universität Berlin, Germany
• Berendsohn W, Anagnostopoulos A, Hagedorn G, Jakupovic J, Nimis PL, Valdés B,
Güntsch A, Pankhurst R, White R, Valdés B, Güntsch A (1999) A Comprehensive
Reference Model for Biological Collections and Surveys. Taxon 48 (3): 511. https://
• FUB, BGBM (2012) Campanula Portal. http://campanula.e-taxonomy.net/. Accessed on:
• Kilian N, Henning T, Plitzner P, Müller A, Güntsch A, Stöver BC, Müller KF, Berendsohn
WG, Borsch T (2015) Sample data processing in an additive and reproducible
taxonomic workﬂow by using character data persistently linked to preserved individual
2Plitzner P et al
specimens. Database: The Journal of Biological Databases and Curation 2015: 1‑19.
• Stöver BC, Müller KF (2015) LibrAlign - A powerful Java GUI library for MSA and
attached raw and meta data. http://www2.ieb.uni-muenster.de/EvolBiodivPlants/en/
Publications/ConferenceContribution?id=100872. Accessed on: 2017-8-15.
The CDM Applied: Unit-Derivation, from Field Observations to DNA Sequences 3