Intern:Experimental data

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Aim
When archiving experimental (biological) data, the origin of experimental organisms should always be provided and included in an event. At the same time, experimental data should be clearly distinguishable from non-experimental data (= field observations). The type of study (field observation, field experiment or laboratory experiment) should be clearly indicated in the PANGAEA record.

To distinguish origin of organisms (as defined in the event) and experimental conditions (coordinates, date/time etc), experiment-specific parameters (e.g. Date of experiments) should be used in the future (for further details, see below).

Dataset attributes?


 * Field observations: Data are either directly collected in the field, or organisms 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 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 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)?

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, include the collection site, 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.
 * For data collected directly in the field (not from experiment), characterize the conditions in the field.
 * Sampling coordinates do not need to be included here, they are given in the event.

Keywords
“Field observation” (if not an experiment)

“Field experiment”

“Mesocosm”

“Laboratory experiment”

“Cultured organism”

“Field-collected organism”

“Ship-based”

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

“Land-based”

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. reflect 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.
 * Event labels for cultured organisms: “species name”_”strain”_”strain nr”
 * 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

 * To specify Method/Device, coordinates and date of the field or laboratory experiments, include methods and the experiment parameters “Date of experiment”, “Latitude of experiment”, “Longitude of experiment”, “Culture location” “Time of organism in laboratory”, “Name of laboratory”, “Name of culture collection”, “Uniform resource locator/link to reference” with a link to the culture collection into the parameter table.
 * Laboratory experiment: Coordinates of the laboratory do not need to be included, but the date/time and coordinates (geocodes) of the sampling event plus the date/time of the experiment.
 * Field experiment: include date/time and coordinates (geocodes) of the event.
 * For experiments, include the column "Type" 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.
 * Include and fill in column “Species, unique identification” with species names, semantic URIs (urns) 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

Use of term-related taxonomic parameters

 * These parameters are of data type 5 (typically named "XXX, unique identification")
 * E.g. "Species, unique identification" (parameter ID 510679), see https://issues.pangaea.de/browse/PMW-2108 or "Taxon/taxa, unique identification" (parameter ID 511751), see https://doi.pangaea.de/10.1594/PANGAEA.958463


 * The "Species, unique identification", for example, allows to use WoRMS or ITIS terminologies which we have in the database, and to configure the columns “Species, unique identification (URI)“ and “Species, unique identification (Semantic URI)“ into the data matrix in addition to the species names.
 * Please do not use the parameter “Uniform resource locator/link to reference” to insert links to the WoRMS or ITIS databases anymore.
 * When other parameters are needed for taxonomic terms (e.g. Order, Family, Genus) these should be created also as term-related parameters of data type ID 5 (ID term).


 * Import:
 * It is necessary to define the terminology for the import routine if species names are used in the data matrix.
 * Column header 510679//#1 will assign WoRMS terms to species names in the data matrix.
 * Column header 510679//#2 will assign ITIS terms to species names in the data matrix.
 * It is possible to enter term IDs or semantic URIs (urns) instead of species names into the import matrix from mixed terminologies. This may be useful if a dataset includes a mix of marine and terrestrial species. (WoRMS focuses on marine species, ITIS includes both terrestrial and marine species.)
 * For this, label the column with the parameter 510679 (“Species, unique identification”) and paste the WoRMS/ITIS specific urns including the species IDs (Aphia IDs or TSNs) in each cell e.g. as follows:
 * WoRMS: urn:lsid:marinespecies.org:taxname:137111
 * ITIS: urn:lsid:itis.gov:itis_tsn:552460
 * When using semantic URIs only in the import matrix, it is not necessary to define the terminology because semantic URIs are unique. For large datasets (thousands of rows) it is however advisable to define the terminology because this saves time during import.
 * Missing terms:
 * If no taxonomic term is available in the external taxonomic terminologies (to check whether terms exist in WoRMS use, the "WoRMS taxon match"; https://www.marinespecies.org/aphia.php?p=match) or in our own term catalogue (you will receive an error message in that case), the respective lines can be left blank. Instead, an additional species text parameter, e.g. "Species" (7053) or "Species Common Name" (48496), with the species/taxa names should be added: e.g. https://doi.pangaea.de/10.1594/PANGEA.958463
 * If a taxonomic is available in the external taxonomic terminologies, but not in our own term catalogue, the terms exist, but are not yet imported in our system (will be updated with a small delay in the order of weeks). In this case missing terms with status „PANGAEA accepted“ with a "preliminary" Aphia-ID/URN (identical to the one given by WoRMS/ITIS) can be created manually. As soon as the terms become available through the updated dumps from WoRMS/ITIS, preliminary terms will be replaced and kept up to date from now on (due to the URN/Aphia-ID).
 * If applicable, the appropriate genus term-parameter can additionally be added, e.g.  https://doi.pangaea.de/10.1594/PANGAEA.951172


 * Configuration in 4D:
 * After import of a dataset it is possible to add the columns “Species, unique identification (URI)“ and “Species, unique identification (Semantic URI)“ to the data matrix. In the Config tab of a dataset, drag and drop parameter “Species, unique identification” from the “Data series” to the “Configuration” field at the bottom to add column (s). In the “Configuration” field right click on one of the “Species, unique identification” data series and choose either “$ (URI)” or “$ (semantic URI)”. Save the dataset.


 * Proofreading and editing:
 * As species names (and other taxonomic terms) are not unique, it is necessary to check whether the correct terms were assigned during import by clicking on the links in the column “Species, unique identification (URI)“ of the dataset on www.pangaea.de (should be done by the dataset author as well!).
 * If necessary, open the data series “Species, unique identification” of the dataset in 4D and select the correct term for the respective data point using the button “Choices”.
 * Helpful links
 * Intern:Import
 * Intern:Terminology Editor

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”, “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 in column, when possible (i.e. only one species studied) species name in parameter names.

-         DateTime of 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”, “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 in column, when possible (i.e. only one species studied) species name in parameter names. -         DateTime of experiment

In situ (field) experiment
o  Mesocosm

o  Other

Title

Abstract

-         Experiment site

Keywords: “In situ experiment” OR “field experiment”, experiment site

Event

-         Reflects location of experiment

-         Label

-         Lat/long

-         DateTime

-         Method/Device: Mesocosm OR field experiment

Data table

-         Species name in column, when possible (i.e. only one species studied) species name in parameter names.

-         DateTime of experiment