=Paper=
{{Paper
|id=Vol-2969/keynote1-s4biodiv
|storemode=property
|title=The Application of Semantic Resources and Technologies for
the Discovery and Integration of Geo- and Biosciences Data (invited paper)
|pdfUrl=https://ceur-ws.org/Vol-2969/keynote1-s4biodiv.pdf
|volume=Vol-2969
|authors=Michael Diepenbroek
|dblpUrl=https://dblp.org/rec/conf/jowo/Diepenbroek21
}}
==The Application of Semantic Resources and Technologies for
the Discovery and Integration of Geo- and Biosciences Data (invited paper)==
https://ceur-ws.org/Vol-2969/keynote1-s4biodiv.pdf
The Application of Semantic Resources and Technologies for the
Discovery and Integration of Geo- and Biosciences Data
Michael Diepenbroek 1
1
MARUM, University of Bremen, Bremen, Germany
Abstract
Large-scale and complex questions in science, such as global warming, invasive species
spread, and resource depletion, increasingly require the collection of disparate data sets from
various data sources building on different knowledge domains in science and society.
Structured data and metadata with consistent semantics are prerequisites for data usability, in
particular for findability of data and efficient data integration. Ontologies, thesauri, and
vocabularies for various science domains have been evolving tremendously during the last
decade and play a key role for the harmonization of data. Nevertheless, the application of
terminologies in the context of data production, archiving, and publication is still at its
beginning. In addition, features and usability of terminology services vary greatly. The
situation is aggravated by the complexity and dynamic growth of measurement and observation
types (parameters) including used methods which are essential for integrating data from
distributed sources.
The ISC World Data Center PANGAEA (www.pangaea.de) with ~200.000 parameters and
methods linked to more than 400.000 data sets covers a large part of scientific fields in the
earth and environmental sciences. For the harmonization of parameters and methods
PANGAEA has (1) embedded a term catalogue (TC) comprising various relevant
terminologies including taxonomies into its editorial system, (2) has conceptualized parameters
and methods by setting up a basic syntax and rule set, and (3) has implemented routines based
on full text search for matching parameter and method names with terms from the TC. Despite
these measures being quite successful it must be noted that the approach is limited to
PANGAEA as a single data provider - the needed effort is high.
More recently, Germany launched the National Research Data Infrastructure (NFDI -
https://www.nfdi.de/) initiative with a number of consortia covering various science domains.
The NFDI4BioDiversity (www.nfdi4biodiversity.org) consortium, having started in 2020,
leads the development of a multi-cloud-based infrastructure supported by almost all existing
consortia. The so-called NFDI Research Data Commons (RDC) will enable uniform access to
data, software, and compute resources as well as sovereign data exchange and collaborative
work. Harmonization of the semantics of data during the ETL process will be supported by
terminology services enhanced by AI technologies. With the RDC, a paradigm shift from data
to function shipping is initiated.
The approach aligns well with initiatives like the European Open Science Cloud, EOSC
(https://eosc-portal.eu/), the NCI RDC (https://datascience.cancer.gov/data-commons) or the
Australian RDC (https://ardc.edu.au/). Nevertheless, integrating and harmonizing data into the
conceived cloud based systems remains a major challenge: (1) Terminology services need to
improve in quality and functionality; (2) AI technologies are not yet part of the integration
process; (3) more convergence towards cross-domain usable metadata standards like
schema.org - allowing community specific extensions like BioSchemas
(https://bioschemas.org/) - is needed to keep the ETL process manageable; and finally (4) a
comprehensible, generally applicable model for the definition of parameters and methods
would make the task considerably easier. The latter should build in part on the UCUM system
(https://ucum.org/) for scientific units. 1
S4BioDiv 2021: 3rd International Workshop on Semantics for Biodiversity, held at JOWO 2021: Episode VII The Bolzano Summer of
Knowledge, September 11-18, 2021, Bolzano, Italy
© 2021 Copyright for this paper by its authors.
Use permitted under Creative Commons License Attribution 4.0 International (CC BY 4.0).
CEUR
Wor
Pr
ks
hop
oceedi
ngs
ht
I
tp:
//
ceur
-
SSN1613-
ws
.or
0073
g
CEUR Workshop Proceedings (CEUR-WS.org)
Bibliography
Dr. Michael Diepenbroek, Geologist and IT Specialist. 1992 PhD in Geology at the Free University
of Berlin; 1992-94 computer center of the AWI, Bremerhaven; 1994-97 conception and implementation
the scientific information system PANGAEA®; 1998-2021 at MARUM, University Bremen, where he
was responsible for the management of PANGAEA®. During the last 10 years he took a leading role
establishing PANGAEA as a global service provider for scientific data, in particular through mandates
from the ISC (ISC World Data System - Vice-Chair of the Scientific Committee 2009-2016), the WMO
(WMO Information System), collaborations with major science publishers, and as Chair/Co-chair in
various RDA groups. Coordinator of the German Federation for Biological Data (GFBio) (2013-2020).
Since 2017 engaged in the National Research Data Infrastructure Initiative (NFDI), in particular in the
conception and preparation of NFDI4BioDiversity (https://www.nfdi4biodiversity.org). Since 2021
working for GFBio e.V. as part of NFDI4BioDiversity.