Intern:Experimental data

Aim
When archiving experimental (biological) data, the origin of experimental organisms/samples should always be provided and included in the Event. At the same time, experimental data should be clearly distinguishable from non-experimental data (= field observations).

To clearly flag experimental datasets, experimental datasets are labelled by using specific keywords, either "Field experiment", "Laboratory experiment" or if not defined which kind of experiment, the generic keyword "Experiment". The addition of additional experimental keywords is possible e.g. "Mesocosm experiment", "Ship-based experiment".

Additionally, every experimental dataset must contain the column/parameter "Type of study" (with the entries "Laboratory experiment" or "Field experiment").

To distinguish the origin of an organism/sample, i.e. sampling time/date and location in the field (as e.g. mentioned in the Event) and experimental conditions (date/time, coordinates of experiment), specific parameters for the experiment date and location are used (e.g. "Sampling date/time, experiment", "Date/time start, experiment", "Date/time end, experiment" or “Latitude, experiment”). For measured variables, no experiment-specific parameters are used. To indicate whether a variable represents adjusted/intended values rather than a measured value, use "Treatment: XY" parameters, e.g., "Treatment: temperature".


 * Field observations: Data are either directly collected in the field, or organisms/samples are collected and preserved (e.g. frozen) for later analysis in the laboratory. E.g. determining the abundance of species in space and time. These are NOT considered experimental data.
 * Field experiments are in situ studies which compare effects on organisms/samples subjected to different treatments in their natural habitat or in conditions resembling their natural habitats. Conditions are partially controlled, the treatments are set up by researchers. E.g. determining growth in different microhabitats.
 * Laboratory experiments are (comparative) studies on organisms/samples under controlled conditions set up in a land-based or mobile (e.g. ship-based) laboratory. E.g. behaviour of fish larvae in response to different treatments of CO2 partial pressure.
 * Computational experiments (i.e. modelling data) are not archived at PANGAEA anymore. Users may be advised to submit to the DKRZ-WDCC https://www.wdc-climate.de/ui/

For further details on the discussion, examples and templates, see https://wiki.pangaea.de/wiki/Biology https://issues.pangaea.de/browse/PEB-213

Abstract

 * In the abstract, it should be specified whether data were collected during a field campaign (non-experimental), a field experiment (e.g., mesocosm) or a land-based or ship-based laboratory experiment. The laboratory should be named.
 * For laboratory experiments on cultured organisms, name the culture collection, where cultured, how long until used for experiment (time, no. of generations if known), and include the culture conditions before and during the experiment.
 * For laboratory experiments on field-collected organisms/samples, include the collection site, conditions in the field, where kept and how long until used for the experiment, specify the culture conditions before and during the experiment.
 * For experimental data from an in situ/field study, give details about the experiment site and conditions before and during the experiment.
 * Sampling coordinates do not need to be included here, they are given in the event.

Keywords
Mandatory:

“Field experiment” or “Laboratory experiment” or "Experiment"

Optional:

“Mesocosm experiment”

“Cultured organism”

“Field-collected organism”

“Ship-based”

“Mobile laboratory”, e.g. ship-based laboratory or laboratory in a van

“Land-based”

“Field observation” (if not an experiment)

Collection/experiment site

Name of laboratory or ship

Events

 * Generally speaking, the origin of experimental organisms should always be stated in the associated event, i.e. latitude/longitude, date/time etc. reflecting the sampling location from the field.
 * If one event is the sampling location of multiple species, this can be added to the event comment (example: https://doi.pangaea.de/10.1594/PANGAEA.921499). In the case of merged samples and if it is not clear which organism is from which location, multiple events can be added to the dataset also after import of the data table.
 * Method/Device of the event should always be equal to the device used to sample the organism from the field. The coordinates and date of the event should always be sampling date and coordinates.
 * Exception: In a field experiment or mesocosm study sampling coordinates are identical to the experiment, or sampling does not really take place. Then use Device “Field experiment” or “Mesocosm (MESO)”, and date/time reflects experiment duration. Example: https://doi.pangaea.de/10.1594/PANGAEA.931402
 * The name of the laboratory should be included in abstract and keywords, but not in the event, unless a "Basis" (e.g. ship) was used to collect the experimental organism. Example: https://doi.pangaea.de/10.1594/PANGAEA.858995

Data table

 * Always include a column with the parameter "Type of study" to the data table, and enter e.g. "Laboratory experiment" or "Field experiment" as values, even if all data are from the same type of study.
 * To distinguish sampling time/date (of original sampling in the field) and experiment time/date, include columns with the parameter “Sampling date/time, experiment” (sampling time during the experiment) or "Date/time start, experiment" and "Date/time end, experiment" in the data table.
 * To indicate whether a variable represents adjusted/intended values rather than a measured value, use "Treatment: XY" parameters, e.g., "Treatment: Temperature, water"
 * Other experiment-specific parameters that can be included are “Latitude, experiment”, “Longitude, experiment”, “Name of laboratory”, “Name of culture collection”, “Uniform resource locator/link to reference” with a link to the culture collection into the parameter table.
 * In addition to the experimental date/time and location parameters, it is possible to configure coordinates and date/time of the event (geocodes) into data table in cases where it makes sense (it would be logical to have both event geocode and experiment date/time and location in data table, but maybe this may be confusing in some datasets)
 * Field experiments: Depth should be included in order to define the medium in which the measurement was performed, even if all observations are from the surface (value = 0; e.g. parameter "DEPTH, water, experiment"). When data are from a depth range, minimum and maximum depths must be provided in separate columns, e.g. "Depth, water, experiment, top/minimum" and "Depth, water, experiment, bottom/maximum".
 * Include term-related taxonomic parameters, e.g. the column “Species, unique identification” with species names, semantic URIs ("Uniform resource name", URN) or term IDs for the WoRMS or ITIS terminologies (see more information below).
 * For genetic data, include the column "Accession number, genetics", and include e.g. NCBI/ENA accession numbers as values. Establish link by entering “insdc:”+accession no. into the cell. For more detail see curator guidelines at Intern:Molecular data in PANGAEA

Laboratory experiment: cultured organism
o  Usually land-based

Title

Abstract

-         Name of culture collection, where cultured, how long until used for experiment (time, no. of generations), culture conditions

Keywords: “Laboratory experiment” (mandatory), “Long-term cultured organism”, name of culture collection, name of laboratory

Event

-         Reflects collection site of original specimen

-         Label

-         Lat/long

-         DateTime

-         Method/Device: sampling device

Data table

-         Species name as term related parameter; if only one species was studied, species name in parameter names

-         Use parameter "Type of study" with entry "laboratory experiment"

-         Date/Time of experiment (Parameter "Sampling time/date, experiment", "Time/date start, experiment", "Time/date end, experiment")

Laboratory experiment: organism collected from the field
o  Land-based lab o  Ship-based or other mobile lab Title Abstract -         Collection site, where kept and how long until used for experiment, culture conditions Keywords: “Laboratory experiment” (mandatory), “field organism”, “land-based” OR “ship-based”, collection site, name of laboratory OR ship Event -         Reflects collection site of specimen -         Label -         Lat/long -         DateTime -         Method/Device: sampling device Data table -         Species name as term related parameter; if only one species was studied, species name in parameter names

-         Use parameter "Type of study" with entry "laboratory experiment"

-         Date/Time of experiment (Parameter "Sampling time/date, experiment", "Time/date start, experiment", "Time/date end, experiment")

In situ (field) experiment
o  Mesocosm

o  Other

Title

Abstract

-         Experiment site

Keywords: "Field experiment" or "In situ experiment” (mandatory), experiment site

Event

-         Reflects location of experiment

-         Label

-         Lat/long

-         DateTime

-         Method/Device: Mesocosm OR field experiment

Data table

-         Species name as term related parameter; if only one species was studied, species name in parameter names

-         Use parameter "Type of study" with entry "field experiment"

-         Date/Time of experiment (Parameter "Sampling time/date, experiment", "Time/date start, experiment", "Time/date end, experiment")