European long-term ecosystem, critical zone and socio-ecological systems research

infrastructure PLUS

Guidelines for data collection

Technical Document

06. October 2020

Author(s) and affiliations: Johannes Peterseil1, Sarah Geiger1, Melanie Tista1

1 Umweltbundesamt GmbH (EAA), Spittelauer Lände 5, 1090 Vienna, Austria

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Prepared under contract from the European Commission Grant agreement No. 871128 EU Horizon 2020 Research and Innovation action Project acronym: eLTER PLUS

Project full title: European long-term ecosystem, critical zone and socio-ecological systems research infrastructure PLUS

Start of the project: Feb 2020 Duration: 60 months

Website: https://www.lter-europe.net/projects/elter-plus Deliverable title: Guidelines for data collection Deliverable n°: Technical document Nature of the deliverable: Report Dissemination level: Public

Citation: Peterseil, J. (2020) Guidelines for data collection. Technical Document, EU Horizon 2020 eLTER PLUS Project, Grant agreement No. 871128.

Deliverable status:

Version Status Date Author(s)

0.1 Draft 19. August 2020 Johannes Peterseil (EAA)

1.0 Final 06.10.2020 Johannes Peterseil & Sarah Geiger

The content of this deliverable does not necessarily reflect the official opinions of the European Commission or other institutions of the European Union.

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Table of Contents

1 Introduction 4

1.1 Purpose of this document 4

2 Data provision workflow 5

2.1 Data Submission Report 7

3 Supported Data formats 8

4 Providing metadata 9

4.1 Keywords 9

4.2 Online distribution link 10

4.3 DEIMS-SDR 10

5 Providing data via Cloud store 10

5.1 Naming convention 10

5.2 EUDAT B2DROP 10

5.3 EUDAT B2SHARE 11

6 Annex – Data requirements 12

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1 Introduction

The eLTER PLUS project is to improve the key infrastructure services of the LTER networks over the coming years. A key objective of this project is to use existing LTER data to address topical scientific research challenges, for example the impact of drought on ecosystem resilience. We aim for a unique holistic approach addressing the research questions in eight case studies focusing on biodiversity, biogeochemical, hydrological and socio-ecological stressors using the diverse resources of the evolving eLTER RI. Data from LTER sites are used to address the research challenges defined by eLTER being

Biodiversity loss

Bio-geochemical processes

Hydrological processes

Socio-ecological systems. Data from a range of sites are required to address cross-site and cross scale analysis. The outcome will be scientific and data publications enabling co-authorship, thereby increasing the visibility eLTER site both individually and as part of the network. In addition eLTER PLUS aims to develop, test and provide central workflows on data validation and harmonisation which aim to support data streams of the upcoming eLTER RI and should service local data management and publication. Data provided are collected in a safe repository only allowing access to the project team and ensuring the property rights and licenses by the data providers.

1.1 Purpose of this document

The aim of the present document is to provide the necessary information the technical workflows of the data provision based on the Virtual Access (VA) and contribution to the project aims. The different specification chapters are structured according to the following information:

Data provision workflow (chapter 2)

Data formats (chapter 3)

Metdadata documentation (chapter 4)

Data provision (chapter 5) Additional supporting documents are provided on the technical description on the provision of data (eLTER_T7.3_Data_Provision_B2SHARE, eLTER_T7.3_Data_Provision_B2DROP) and authoring of metadata (eLTER_T7.3_Metadata_Provision_DEIMSSDR). For general questions, please contact

● Johannes Peterseil (Johannes.Peterseil@Umweltbundesamt.at ) or ● Herbert Haubold (Herbert.haubold@umweltbundesamt.at )

Technical information can be provided by

● Sarah Geiger (sarah.geiger@umweltbundesamt.at) ● Melanie Tista (melanie.tista@umweltbundesamt.at) ● Christoph Wohner (christoph.wohner@umweltbundesamt.at) ● Johannes Peterseil (Johannes.Peterseil@Umweltbundesamt.at)

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2 Data provision workflow

The entity for data provision is a data package, which contains the data files (one or more containing defined data, e.g. time slices) and, if required, the descriptive meta-information (e.g. station, method). This is either provided as single zip-file or located in a specific directory.

Figure 1 provides a schematic overview on the data provision workflow

Figure 1 Structure of the data provision

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The data provision workflow consists of the following steps:

1) Data needs to be provided in pre-defined data formats.

If data are already structured following well-established data formats, (e.g. ICP Integrated Monitoring, ICP Forest, IC Water, ICOS Ecosystem, Darwin Core) these well-established data formats are used. The selected data format needs to be mentioned in the data submission report (INST_DataSubmissionReport_DATE).

If data are not structured according to well established data formats, the eLTER Data Specification needs to be applied (see table 2).

2) Data need to be provided using a shared web link for download. The data can either be open access or only to be used internally. The data usage needs to be described in the metadata (e.g. license).

Data can be provided using a public or private accessible cloud repository provided by the data provider. The download link needs to be recorded in the data submission report.

If no cloud repository can be provided by the data provider, the use of B2DROP (https://b2drop.eudat.eu/, based on NextCloud) or B2SHARE (https://b2share.eudat.eu, public archive) is recommended. The download link needs to be recorded in the data submission report.

3) A data package needs to be described by open accessible metadata. The metadata needs to be provided in English to ensure the usability.

If descriptive metadata are already provided in a local metadata catalogue, the link to the publically available metadata URL is provided in the data submission report.

If no metadata are provided or metadata are provided in local languages, the data (package) needs to documented on DEIMS-SDR (https://deims.org)

4) For each data submission a Data Submission Report file on the data provided needs to be sent.

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2.1 Data Submission Report

For each data submission, a Data Submission Report (as Excel file) needs to be generated and sent via e-mail. The report contains information on data packages provided including contact information. This information is only used for internal reporting purposes on the data collection for the project.

Table 1 provides an overview on the fields to be provided for the Data Submission Report.

Table 1 Data provision protocol file – core fields

Field name Field description Field type Example

ORG_NAME Name of institution Text UTF-8 Umweltbundesamt

CONTACT_NAME Name of data provider Text UTF-8 Johannes Peterseil

CONTACT_EMAIL Email of data provider email-adress

Johannes.peterseil@umweltbundesamt.at

DATE_PUBLICATION Date of publication/ provision YYYY-MM-DD

2020-09-30

DATA_VERSION Individual code assigned to the data set by the data provider

number 1.0

GENERAL_COMMENTS Any comments related to the entire data set

Text UTF-8 data for plots uploaded

SITE_CODE Reference to the LTER site providing the deims.id accessible through https://deims.org

URL https://deims.org/8eda49e9-1f4e-4f3e-b58e-e0bb25dc32a6

METADATA_URL Reference to the metadata record describing the data files or data package, e.g. link to deims.org MD record (URL) or accessible metadata catalogue

URL https://deims.org/dataset/cfc1a860-840a-41f2-a208-cf66ab25dfa4

DATA_URL Link (URL) to the download location for the data files or data package, e.g. B2DROP or private Cloud store

URL http://hdl.handle.net/11097/71e09618-f769-4f99-a96f-fd6f90135011

DATA_FORMAT Comments on the data reporting format used, e.g. ICP Forest

Text UTF-8 eLTER Data Reporting V1.3

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3 Supported Data formats

Transformation of data formats for data providers should be avoided as far as possible. Therefore a number of suggested data formats are provided in Table 2. If data cannot be provided in this recommended format, we ask to use the eLTER Data Specfication for observation data. Table 2 Recommended data formats for data provision

Name URL Format

ICP Integrated Monitoring

https://www.syke.fi/en-US/Research__Development/Nature/Monitoring/Integrated_Monitoring/Manual_for_Integrated_Monitoring/7_Methodology_and_Reporting_of_Subprogrammes

csv, xls

ICP Forests http://icp-forests.net/page/data-submission https://icp-forests.org/documentation/Surveys/index.html https://icp-forests.org/documentation/Introduction/General_remarks.html https://icp-forests.org/documentation-adds/csv-templates/csv_templates.zip

csv

ICP Waters http://www.icp-waters.no/data/submit-data/

eLTER Data Specification

(Data specification) https://drive.google.com/file/d/1ud7ZKScn3k5PUW0_QvA1JzBpg9iX1UC7/view?usp=sharing (Template) https://drive.google.com/file/d/15F0PeE4VVWpTFnSeQ17ahGqNSssi0CAf/view?usp=sharing

csv, xls

Biodiversity (DwC Event)

csv

OGC WFS/WMS gml, xml

OGC SOS xml

Spatial data vector gdb, shp, OGC WFS

Spatial data raster geoTiff, raster, OGC WMS

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4 Providing metadata

A minimum set of metadata needs to be provided for the data package:

Data set title

Reference to the LTER site (deims.id see https://deims.org)

Abstract

Data range

Data set owner and contact

Keywords (see also below)

Parameters observed

Geographic context of the dataset (bounding box)

Online distribution link (see also below)

Method description

Data policy

4.1 Keywords

It is important that you add the keyword “eLTER PLUS VA” to your dataset as this is needed to easily identify datasets that have been shared within the eLTER PLUS project.

Additionally, a keyword describing the data topic is needed, those being:

● Biodiversity

● Biomass

● Climate

● Atmospheric deposition

● Soil-atmosphere gas exchange

● Air quality

● Soil climate

● Solid soil chemistry

● Soil water

● Runoff, streams and standing water

● Groundwater

● Land use

● Socio-economy

● Topography

● Vegetation

● Soil physics

● Land cover

● Habitat diversity

● Remote sensing

An example for proper usage of keywords for a dataset would be: “eLTER VA PLUS” “Vegetation” „ground vegetation“ „understory vegetation“ „forest vegetation“

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4.2 Online distribution link

In case data are not shared via a public repository and have restricted use in the eLTER PLUS project, in the Online distribution link the email to the contact person needs to be provided.

Nevertheless, in the data Submission Report the download link to the data files need to be provided. These links are not shared and used only for project purposes.

4.3 DEIMS-SDR

DEIMS-SDR (https://deims.org) is the central metadata catalogue for eLTER. It allows to document research sites as well as related datasets. In case metadata are not provided via an alternative catalogue the data packages needs to documented in DEIMS-SDR.

A short description on how to use DEIMS-SDR and how to obtain a user account is provided in the document eLTER_T7.3_Metadata_Provision_DEIMSSDR.

5 Providing data via Cloud store

5.1 Naming convention

The naming convention for files is: Template: [2-digit Country code]_[LTER Site Name]_[Data group] _[Variable group]_[Time span]_[Version]

Example: AT_ZOEBELBODEN_VEG_SPECCOVER_2015_V20170315

Element Description Example

2-digit Country code

Reference to the country of the site as two-digit country code according to ISO 3166-1 alpha-2

AT

LTER Site Code Name of the site according to DEIMS-SDR, if the name is too long the site name can be shortened

ZOEBELBODEN

Data Topic Max 5-digit code for data topic or observation programme, e.g. METEO (Meteorology), BIODIV (biodiversity), DEPO (deposition), GHG (Green House gas), SW (Soil water). The abbreviation is defined by the data provider depending on the data.

VEG

Variable group Optional, list of variables or variable groups contained in the data. The abbreviation is defined by the data provider depending on the data.

SPECCOVER

Time span Time span covered in the data 2015

Version Data version in the format “V”YYYYMMDD V20170315

5.2 EUDAT B2DROP

B2DROP (https://b2drop.eudat.eu/) is a fully secured data exchange service on the basis of a NextCloud server. During transmission data are encrypted through the exclusive use of the https protocol for data transfer. Access to the data is only given to project members of the eLTER project. Additional documentation can be found at https://eudat.eu/services/userdoc/b2drop.

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A short description on how to use B2DROP is provided in document eLTER_T7.3_Data_Provision_B2DROP.

5.3 EUDAT B2SHARE

B2SHARE (https://b2share.eudat.eu) allows the upload of data files to a web repository. B2SHARE is developed and by the EUDAT2020 project in order to provide a common data infrastructure for European research data. eLTER PLUS is using the services provided by the EUDAT2020 project in order to share and publish data files. When uploading data files to B2SHARE a PID (Persistent Identifier) and DOI (Digital Object Identifier) is created to allow an unambiguous identification of the file including a resolution service for the PID. B2SHARE supports an open data policy, allowing implementing a retention period. A data file uploaded to the B2SHARE repository needs to be accompanied by a metadata record in DEIMS-SDR describing the observation context. A short description on how to use B2SHARE is provided in the document eLTER_T7.3_Data_Provision_B2SHARE.

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6 Annex – Data requirements

Following variables were indicated in the data requirements. Please check with your answers in the data availability survey.

Type Group Variable Unit Temporal resolution

BIO

_T8_1

BG

C_T8

_2

CW

F_T8_3

SES_T8_4

BIO

_T9_1

BG

C_T9

_2

CW

F_T9_3

SES_T9_4

TimeSeries

Biodiversity

all taxonomic groups

occurrence/abundance/composition/biomass

annual x x

TimeSeries

Biomass Terrestrial aboveground biomass

kg*m-2 annual x x

TimeSeries

Biomass Terrestrial aboveground vegetation growth

kg*m-2 monthly/annual

x x

TimeSeries

Biomass Terrestrial net primary production

kgC*m-2 daily/monthly/annual

x x x x x x

TimeSeries

Biomass Terrestrial gross primary production

kgC*m-2 daily/monthly/annual

x x x x x x

TimeSeries

Biomass Leaf area Index (LAI)

unitless daily/monthly/annual

x x x x x

TimeSeries

Biomass Tissue (Leaf) C and N content

% annual x x

TimeSeries

Biomass Aboveground litterfall

kg*m-2 monthly/annual

x x

TimeSeries

Biomass Belowground (soil) litterfall

kg*m-2 monthly/annual

x x

TimeSeries

Climate Air temperature °C 30 min x x x x x x x x

TimeSeries

Climate Precipitation mm 30 min x x x x x x x x

TimeSeries

Climate Relative air humidity

% 30 min x x x x

TimeSeries

Climate Wind speed / Wind direction

m*s-1, ° 30 min x x

TimeSeries

Climate Surface atmospheric pressure

mbar 30 min x x

TimeSeries

Climate Photosynthetic Active Radiation

W*m-2 or PPFD 30 min x x x

TimeSeries

Climate Direct incoming short wave radiation

W*m-2 30 min x x x

TimeSeries

Climate Reflected short wave radiation

W*m-2 30 min x x

TimeSeries

Climate Diffused long-wave radiation from the sky

W*m-2 30 min x x

TimeSeries

Climate Diffused long-wave radiation from the surface

W*m-2 30 min x x

TimeSeries

Atmospheric deposition

Bulk NH4-N, NO3-N, Ntot deposition in precipitation

kg*ha-1 monthly x x x x

TimeSeries

Atmospheric deposition

Bulk P deposition in precipitation

kg*ha-1 monthly x x x x

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Type Group Variable Unit Temporal resolution

BIO

_T8_1

BG

C_T8

_2

CW

F_T8_3

SES_T8_4

BIO

_T9_1

BG

C_T9

_2

CW

F_T9_3

SES_T9_4

TimeSeries

Atmospheric deposition

Bulk K deposition in precipitation

kg*ha-1 monthly x x x x

TimeSeries

Atmospheric deposition

Bulk NH4-N, NO3-N, Ntot deposition in canopy throughfall (forests)

kg*ha-1 monthly x x x x

TimeSeries

Atmospheric deposition

Bulk P deposition in canopy throughfall (forests)

kg*ha-1 monthly x x x x

TimeSeries

Atmospheric deposition

Bulk K deposition in canopy throughfall (forests)

kg*ha-1 monthly x x x x

TimeSeries

Atmospheric deposition

NH4-N, NO3-N, Ntot deposition in stemflow (forests)

kg*ha-1 monthly x x x x

TimeSeries

Atmospheric deposition

P deposition in stemflow (forests)

kg*ha-1 monthly x x x x

TimeSeries

Atmospheric deposition

K deposition in stemflow (forests)

kg*ha-1 monthly x x x x

TimeSeries

Atmospheric deposition

Dry deposition of Nitrogen

kg*ha-1 monthly x x x x

TimeSeries

Soil-atmosphere gas exchange

Eddy covariance flux data product (compatible with ICOS L2, Ameriflux, Fluxnet)

various various x x

TimeSeries

Soil-atmosphere gas exchange

Soil CO2 flux gC*m-2 daily/monthly/annual

x x

TimeSeries

Soil-atmosphere gas exchange

Soil CH4 flux gC*m-2 daily/monthly/annual

x x

TimeSeries

Soil-atmosphere gas exchange

Soil N2O, NO, NOx flux

gC*m-2 daily/monthly/annual

x x

TimeSeries

Air quality

Ozone concentration

ppm 30 min x x

TimeSeries

Air quality

NOx concentration

mg*m-3 30 min x x

TimeSeries

Air quality

NH3 concentration

mg*m-3 30 min x x

TimeSeries

Soil climate

Soil temperature °C 30 min x x x x x

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Type Group Variable Unit Temporal resolution

BIO

_T8_1

BG

C_T8

_2

CW

F_T8_3

SES_T8_4

BIO

_T9_1

BG

C_T9

_2

CW

F_T9_3

SES_T9_4

TimeSeries

Soil climate

Soil water content Vol% 30 min x x x x x x

TimeSeries

Solid soil chemistry

Soil organic C content (per horizon)

mg*kg-1 annual x x x x x x

TimeSeries

Solid soil chemistry

Soil total N content (per horizon)

mg*kg-1 annual x x x x x x

TimeSeries

Solid soil chemistry

Soil total P content (per horizon)

mg*kg-1 annual x x x x x x

TimeSeries

Solid soil chemistry

Soil total K content (per horizon)

mg*kg-1 annual x

TimeSeries

Solid soil chemistry

Soil pH (in H2O/KCl/CaCl2) (per horizon)

unitless annual x x x x x x

TimeSeries

Solid soil chemistry

Soil cation exchange capacity (per horizon)

cmolc*kg-1 annual x x x x x x

TimeSeries

Solid soil chemistry

Soil base saturation (per horizon)

% annual x x x x x

TimeSeries

Soil water

NH4-N, NO3-N, DON concentration

mg*l-1 monthly x x x x

TimeSeries

Soil water

NH4-N, NO3-N, DON leaching

kg*ha-1 monthly x x x x

TimeSeries

Soil water

DOC concentration

mg*l-1 monthly x x x x

TimeSeries

Soil water

DOC leaching kg*ha-1 monthly x x x x

TimeSeries

Soil water

Percolation mm monthly x x x x

TimeSeries

Runoff, streams and standing water

TOC, DOC concentration

mg*l-1 monthly or higher frequency

x x x

TimeSeries

Runoff, streams and standing water

Ntot, NH4-N, NO3-N concentration

mg*l-1 monthly (or finer)

x x x x x

TimeSeries

Runoff, streams and standing water

P concentration mg*l-1 monthly (or finer)

x x x x x

TimeSeries

Runoff, streams and standing water

Cation concentrations

mg*l-1 monthly (or finer)

x x x

TimeSeries

Runoff, streams

Anion concentrations

mg*l-1 monthly (or finer)

x x

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Type Group Variable Unit Temporal resolution

BIO

_T8_1

BG

C_T8

_2

CW

F_T8_3

SES_T8_4

BIO

_T9_1

BG

C_T9

_2

CW

F_T9_3

SES_T9_4

and standing water

TimeSeries

Runoff, streams and standing water

pH value unitless monthly (or finer)

x x x

TimeSeries

Runoff, streams and standing water

Conductivity mS*m-1 monthly (or finer)

x x x x

TimeSeries

Runoff, streams and standing water

Discharge l*s-1 monthly (or finer)

x x x x

TimeSeries

Runoff, streams and standing water

Water temperature

°C monthly (or finer)

x x

TimeSeries

Runoff, streams and standing water

Pesticides mg*l-1 monthly (or finer)

x x

TimeSeries

Runoff, streams and standing water

Transparency m monthly (or finer)

x x

TimeSeries

Groundwater

Groundwater table height

cm monthly (or finer)

x x x x

TimeSeries

Groundwater

Cation concentrations

mg*l-1 monthly (or finer)

x x x

TimeSeries

Groundwater

Anion concentrations

mg*l-1 monthly (or finer)

x x

TimeSeries

Land use

N, P, K fertilisation

kg*m-2 annual x x x x x

TimeSeries

Land use

Liming kg*m-2 annual x x x x x

TimeSeries

Land use

Pesticides kg*m-2 annual x x x x x

TimeSeries

Land use

Grazing timing, stocking intensity, animal

time*yr-1, LU*ha-1 annual x x x x x x

TimeSeries

Land use

Crop, grassland harvesting

kg*m-2 annual x x x x x x

TimeSeries

Land use

Forest planting, thinning, clearcut

number/m³*ha-1 annual x x x x x x

TimeSeries

Land use

Irrigation timing, amount

m³*event annual x x x x

TimeSeries

Land use

Vistors number annual x x

TimeSeries

Socio-economy

Gross domestic product

EUR decadal x x x

TimeSeries

Socio-economy

Governance structure and character

descriptive decadal x x

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Type Group Variable Unit Temporal resolution

BIO

_T8_1

BG

C_T8

_2

CW

F_T8_3

SES_T8_4

BIO

_T9_1

BG

C_T9

_2

CW

F_T9_3

SES_T9_4

TimeSeries

Socio-economy

Demography tbd decadal x x x

TimeSeries

Socio-economy

Property ownership/laws/institutions

tbd decadal x x

Descriptive

Topography

elevation, slope, aspect

m, °, ° x x

Descriptive

Vegetation

Forest stand age yr x x x x

Descriptive

Soil physics

Soil type categories x x x x x

Descriptive

Soil physics

Parent material (geology)

categories x x x x x

Descriptive

Soil physics

Soil bulk density g*cm-3 x x x x

Descriptive

Soil physics

Soil depth (per horizon)

cm x x x x

Descriptive

Soil physics

Soil fractions (Water stable aggregate fractionation)

% per fraction x x

Descriptive

Soil physics

Soil texture categories x x x x

Descriptive

Soil physics

Soil stone content (>2mm)

% x x x x

Descriptive

Soil physics

Soil water retention capacity (water retention curves; field capacity, water saturation, wilting point)

mm*cm-1 x x x x

Descriptive

Soil physics

Saturated hydraulic conductivity

m*s-1 x x x x

Descriptive

Land cover

Land cover categories x x x x x x x x

Descriptive

Land use

Crop type categories x x

Descriptive

Land use

Fire regime categories x

Descriptive

Land use

Forest management

categories x

Descriptive

Land use

Land use (historic) descriptive x x x

Descriptive

Land use

Land use change descriptive x x x

Descriptive

Habitat diversity

River Habitat Survey (RHS) information

categories x

Descriptive

Habitat diversity

Habitat map/list categories x

Remote Sensing

Remote sensing

Productivity (NDVI)

x

Remote Sensing

Remote sensing

Phenology/Seasonality

x

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Type Group Variable Unit Temporal resolution

BIO

_T8_1

BG

C_T8

_2

CW

F_T8_3

SES_T8_4

BIO

_T9_1

BG

C_T9

_2

CW

F_T9_3

SES_T9_4

Remote Sensing

Land cover

CORINE Land cover (or similar)

categories x x x x x x x x