Biodiversity Information Science and Standards :
Conference Abstract
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Corresponding author: Katrina Exter (katrina.exter@vliz.be)
Received: 24 Sep 2020 | Published: 09 Oct 2020
© 2020 Katrina Exter, Cedric Decruw, Marc Portier, Vasilis Gerovasileiou, Christina Pavloudi, Matthias Obst
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:
Exter K, Decruw C, Portier M, Gerovasileiou V, Pavloudi C, Obst M (2020) Genomics Observatory Use-Case: The challenge to standardise image and sequence data to Darwin Core format. Biodiversity Information Science and Standards 4: e58938. https://doi.org/10.3897/biss.4.58938
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Genomic Observatories (GOs) are an increasingly important resource to study the effect of climate change on marine populations. The data gathered by GOs allow one to map and track how marine populations change with time and location, and how those changes relate to the local and global conditions. Such data may be used to calculate Essential Biodiversity Variables (EBVs) and can provide important information for predictive modelling of marine biodiversity.
GOs are sites that are subject to long-term scientific research, including (but not limited to) the sustained study of genomic biodiversity from single-celled microbes to multicellular organisms. We are involved in a number of GO projects, including:
The data collected from these GOs are not particularly complicated: sampling and sequencing protocols are well established and the images are taken with standard cameras. However, complexity arises when
We also want to be able to compare data between different GO projects, and to be able to incorporate measurements from nearby monitoring stations, as this will allow for an enhanced analysis of the evolution of marine benthic populations in light of climate change.
Our aim is to adopt the Darwin Core Archive (DwC-A) OBIS-ENV-DATA format for the data from ARMS-MBON and OSD, including the linkages to the images and sequences. ARMS-MBON presents a challenge because of the wide range of data collected. Our use-case for the data format we require contains the following elements:
Clearly, a high degree of data standardisation is necessary to enable harmonisation of the data, to accommodate the multiple streams of linked data values, which will be added by multiple creators and users of the data.
genomics observatories, Darwin Core Archive, imaging data, DNA sequences, species occurrence
Katrina Exter
TDWG 2020
ASSEMBLE Plus: OSD and ARMS receive funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 730984.
EMBRC: The OSD and ARMS projects are supported by the European Marine Biology Resource Centre
EMODNet Biology: This work has been financially supported by the EC DG-MARE (EMODnet Observation and Data network - Lot5 - Biology: EASME/EMFF/2016/1.3.1.2/Lot5/SI2.750022).