PANGAEA Wiki - User contributions [en]

Experimental data

2026-03-24T15:13:14Z

Awittmann: Corrected typo

This wiki article describes guidelines on how to prepare experimental data for submission to PANGAEA. Please read our [[Authors Guides]] first. They provide general guidelines on how to prepare your metadata and data for publication in PANGAEA. Check if your experimental data file types and format are accepted by PANGAEA (see [[Authors Guides#Data types and file formats accepted by PANGAEA|respective section in our Authors Guides]]). In addition, you can find the template for experimental data in section 2 (coming soon) and the specific requirements for experimental (meta-)data in section 3 below. If you are dealing with biological experimental data, please also have a look at our specific guidelines for [[Biology]].

== Types of experimental data at PANGAEA ==
Experimental data are collected in a structured trial to test a hypothesis by manipulating variables (treatments) and observing their effects on organisms or environmental samples under (semi-)controlled conditions in natural or artificial settings. Experiments are conducted in multiple research domains, and diverse experimental set-ups exist. The main types of experiments can be summarized as:

'''a) Field experiments''' are ''in situ'' studies designed to compare the effects of different treatments on organisms or other samples in their natural environment or under conditions that closely resemble it. Conditions are partially controlled and the treatments are set up by researchers, e.g. to investigate the growth of an organism in different microhabitats. This also includes mesocosm studies with an open experimental set-up that is influenced by several external environmental factors.

Example datasets:

* Biodiversity experiment: https://doi.org/10.1594/PANGAEA.967077
* Benthocosm experiment: https://doi.org/10.1594/PANGAEA.974781

'''b) Enclosed outdoor experiments''' are set up outside in a closed experimental system, e.g. greenhouse studies or bottle experiments. External factors are better controlled in these systems and therefore the studied sample or organism is less influenced by external environmental factors than in field studies. Relevant environmental factors for these outdoor experiments may e.g. include the natural daily cycle of light or air temperature.

Example datasets:

* Greenhouse experiment: https://doi.org/10.1594/PANGAEA.973270
* Ex-situ cultivation system & subsequent outdoor bottle incubation: https://doi.pangaea.de/10.1594/PANGAEA.973666

'''c) 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 carbon dioxide (CO2) partial pressure.

Example datasets:

* Culture experiments with phytoplankton: https://doi.org/10.1594/PANGAEA.964086
* Incubation experiments with sediments: https://doi.org/10.1594/PANGAEA.977247
* Laboratory experiments with artificial kelp/simulated water flow: https://doi.pangaea.de/10.1594/PANGAEA.971269

The following data '''are not considered''' experimental data in PANGAEA:
* '''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. to determine the abundance of species in space and time. For the submission of field observation data, have a look at our general and domain-specific templates: [[Best practice manuals and templates]].
* '''Computational experiments''' (e.g. modelling data) are only archived at PANGAEA, if a direct relation to a corresponding environmental study exists. For further details, see our article [[Model data and PANGAEA]].

== Template for experimental data ==
coming soon

== Specific requirements for metadata and data ==

=== Metadata - Abstract ===

* For general guidelines, please read: [[Abstract]].
* Describe '''how the experiment was carried out''', and include the '''conditions/treatments before and during''' the experiment.
* Specify the '''type of experiment''' and the '''location''' where the experimental data were collected, e.g. "field experiment in the Wadden Sea at Spiekeroog", or "laboratory experiment at the Marine Biology laboratory at Kiel University".

=== Metadata - Keywords ===
It is '''mandatory to include ONE of the following keywords''' for experimental data to distinguish them from other datasets with field observations in PANGAEA:

* Field experiment
* Laboratory experiment
* Mesocosm experiment
* Greenhouse experiment
* Experiment
Further keywords, such as “ship-based”, “land-based”, the name of the experimental site or the analysed sample/species may be included in addition.

=== Metadata - Event table ===
The Event table (see template, coming soon) gives an overview when, where and how the experimental sample, organism or data was collected. Please provide the following event information:

* '''Event(s) for the actual experiments''' including the location and the start and end date/time of the experiments
* If available, additionally provide the '''original sampling event''' of the studied sample/organism in the field prior to the experiments
For general information regarding the event information, please read: [[Event]]. Please use one of the following methods for the events of the actual experiments: “Field experiment”, “Laboratory experiment”, “Mesocosm experiment”, “Greenhouse experiment”, “Experiment”.

=== Metadata - Parameter table ===
This table summarizes all variables (PANGAEA "[[Parameter|parameters]]") that are included in the data table, specifies units, principal investigator(s) and the methods used to generate the data. Please read our [[Authors Guides#Requirements for the data files and their metadata|general requirements for parameter information]] and see our respective template (coming soon). Specific requirements for experimental data include:

* The parameter name should specify whether the values in a column reflect an '''experimental condition/treatment''' '''or a measured variable'''. For treatment parameters, use the syntax '''Treatment: XY''', e.g., "Treatment: temperature", “Treatment: light intensity”, or “Treatment: carbon dioxide”.
* The parameter name may include the type of sample or species name, e.g. “Mytilus edulis, wet mass“.

=== Data table/files ===
Prepare your data according to our general requirements for [[Authors Guides#How to prepare tabular Data:|tabular data]] and [[Authors Guides#How to prepare binary files:|binary files]]. Specific requirements for tabular experimental data include:

* The '''first column''' must be the '''Event label'''. The Event label must correspond to the event information of the actual experiments included in the Event table.
* The '''second column''' must be '''"Type of study'''" to separate experimental datasets from field observations. Use e.g. "Laboratory experiment" or "Field experiment" as values, even if all data are from the same type of study.
* If an organism (e.g. Mytilus edulis) was investigated in the experiment, the species should be indicated in the parameter names. Alternatively, if multiple species were studied, include e.g. the '''column "Species, unique identification"''' for the scientific name of the species even if only one species was studied. Please provide a [https://en.wikipedia.org/wiki/LSID Life Science Identifier] (LSID e.g. <nowiki>urn:lsid:marinespecies.org:taxname:140656</nowiki>) in a '''separate column''', e.g. “'''Species, unique identification (Semantic URI)'''”. We recommend to use [https://www.marinespecies.org/index.php WoRMS] LSIDs for marine organisms or [https://www.itis.gov/ Integrated Taxonomic Information System] (ITIS) LSIDs for terrestrial and limnic organisms.
* Any other type of studied samples (e.g. sediment) can either be indicated in the parameter names or alternatively specified in the '''column "Sample type"'''.
* Include the '''date/time of experiment''' in '''ISO-format''' and as '''UTC''' (use e.g. parameter "Sampling date/time, experiment" or "Date/time start, experiment", "Date/time end, experiment"). Start and end date/time must be provided in separate columns.
* '''For field experiments, include the parameters Latitude and Longitude''' in decimal degrees, and the third dimension '''depth''' (e.g. parameters “Depth, sediment, experiment [m]”, "Depth, water, experiment [m]"), even if all observations are from the surface (value = 0). When data are from a depth range, minimum and maximum depths must be provided in separate columns.
* Use "'''Treatment: XY" parameters''', e.g., "Treatment: Temperature, water" to indicate the experimental conditions/treatments for the data.

Experimental data

2026-03-24T15:11:30Z

Awittmann: Edited definition of "experiment"/"experimental data"

This wiki article describes guidelines on how to prepare experimental data for submission to PANGAEA. Please read our [[Authors Guides]] first. They provide general guidelines on how to prepare your metadata and data for publication in PANGAEA. Check if your experimental data file types and format are accepted by PANGAEA (see [[Authors Guides#Data types and file formats accepted by PANGAEA|respective section in our Authors Guides]]). In addition, you can find the template for experimental data in section 2 (coming soon) and the specific requirements for experimental (meta-)data in section 3 below. If you are dealing with biological experimental data, please also have a look at our specific guidelines for [[Biology]].

== Types of experimental data at PANGAEA ==
Experimental data are collected in a structured trial to test a hypothesis by manipulating variables (treatments) and observing their effects on organisms or environmental samples under (semi-)controlled conditions in natural or artificial settings. Experiments are conducted in multiple research domains, and diverse experimental set-ups exist. The main types of experiments can be summarized as:

'''a) Field experiments''' are ''in situ'' studies designed to compare the effects of different treatments on organisms or other samples in their natural environment or under conditions that closely resemble it. Conditions are partially controlled and the treatments are set up by researchers, e.g. to investigate the growth of an organism in different microhabitats. This also includes mesocosm studies with an open experimental set-up that is influenced by several external environmental factors.

Example datasets:

* Biodiversity experiment: https://doi.org/10.1594/PANGAEA.967077
* Benthocosm experiment: https://doi.org/10.1594/PANGAEA.974781

'''b) Enclosed outdoor experiments''' are set up outside in a closed experimental system, e.g. greenhouse studies or bottle experiments. External factors are better controlled in these systems and therefore the studied sample or organism is less influenced by external environmental factors than in field studies. Relevant environmental factors for these outdoor experiments may e.g. include the natural daily cycle of light or air temperature.

Example datasets:

* Greenhouse experiment: https://doi.org/10.1594/PANGAEA.973270
* Ex-situ cultivation system & subsequent outdoor bottle incubation: https://doi.pangaea.de/10.1594/PANGAEA.973666

'''c) 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 carbon dioxide (CO2) partial pressure.

Example datasets:

* Culture experiments with phytoplankton: https://doi.org/10.1594/PANGAEA.964086
* Incubation experiments with sediments: https://doi.org/10.1594/PANGAEA.977247
* Laboratory experiments with artificial kelp/simulated water flow: https://doi.pangaea.de/10.1594/PANGAEA.971269

The following data '''are not considered''' experimental data in PANGAEA:
* '''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. to determine the abundance of species in space and time. For the submission of field observation data, have a look at our general and domain-specific templates: [[Best practice manuals and templates]].
* '''Computational experiments''' (e.g. modelling data) are only archived at PANGAEA, if a direct relation to a corresponding environmental study exists. For further details, see our article [[Model data and PANGAEA]].

== Template for experimental data ==
coming soon

== Specific requirements for metadata and data ==

=== Metadata - Abstract ===

* For general guidelines, please read: [[Abstract]].
* Describe '''how the experiment was carried out''', and include the '''conditions/treatments before and during''' the experiment.
* Specify the '''type of experiment''' and the '''location''' where the experimental data were collected, e.g. "field experiment in the Wadden Sea at Spiekeroog", or "laboratory experiment at the Marine Biology laboratory at Kiel University".

=== Metadata - Keywords ===
It is '''mandatory to include ONE of the following keywords''' for experimental data to distinguish them from other datasets with field observations in PANGAEA:

* Field experiment
* Laboratory experiment
* Mesocosm experiment
* Greenhouse experiment
* Experiment
Further keywords, such as “ship-based”, “land-based”, the name of the experimental site or the analysed sample/species may be included in addition.

=== Metadata - Event table ===
The Event table (see template, coming soon) gives an overview when, where and how the experimental sample, organism or data was collected. Please provide the following event information:

* '''Event(s) for the actual experiments''' including the location and the start and end date/time of the experiments
* If available, additionally provide the '''original sampling event''' of the studied sample/organism in the field prior to the experiments
For general information regarding the event information, please read: [[Event]]. Please use one of the following methods for the events of the actual experiments: “Field experiment”, “Laboratory experiment”, “Mesocosm experiment”, “Greenhouse experiment”, “Experiment”.

=== Metadata - Parameter table ===
This table summarizes all variables (PANGAEA "[[Parameter|parameters]]") that are included in the data table, specifies units, principal investigator(s) and the methods used to generate the data. Please read our [[Authors Guides#Requirements for the data files and their metadata|general requirements for parameter information]] and see our respective template (coming soon). Specific requirements for experimental data include:

* The parameter name should specify whether the values in a column reflect an '''experimental conditions/treatment''' '''or a measured variable'''. For treatment parameters, use the syntax '''Treatment: XY''', e.g., "Treatment: temperature", “Treatment: light intensity”, or “Treatment: carbon dioxide”.
* The parameter name may include the type of sample or species name, e.g. “Mytilus edulis, wet mass“.

=== Data table/files ===
Prepare your data according to our general requirements for [[Authors Guides#How to prepare tabular Data:|tabular data]] and [[Authors Guides#How to prepare binary files:|binary files]]. Specific requirements for tabular experimental data include:

* The '''first column''' must be the '''Event label'''. The Event label must correspond to the event information of the actual experiments included in the Event table.
* The '''second column''' must be '''"Type of study'''" to separate experimental datasets from field observations. Use e.g. "Laboratory experiment" or "Field experiment" as values, even if all data are from the same type of study.
* If an organism (e.g. Mytilus edulis) was investigated in the experiment, the species should be indicated in the parameter names. Alternatively, if multiple species were studied, include e.g. the '''column "Species, unique identification"''' for the scientific name of the species even if only one species was studied. Please provide a [https://en.wikipedia.org/wiki/LSID Life Science Identifier] (LSID e.g. <nowiki>urn:lsid:marinespecies.org:taxname:140656</nowiki>) in a '''separate column''', e.g. “'''Species, unique identification (Semantic URI)'''”. We recommend to use [https://www.marinespecies.org/index.php WoRMS] LSIDs for marine organisms or [https://www.itis.gov/ Integrated Taxonomic Information System] (ITIS) LSIDs for terrestrial and limnic organisms.
* Any other type of studied samples (e.g. sediment) can either be indicated in the parameter names or alternatively specified in the '''column "Sample type"'''.
* Include the '''date/time of experiment''' in '''ISO-format''' and as '''UTC''' (use e.g. parameter "Sampling date/time, experiment" or "Date/time start, experiment", "Date/time end, experiment"). Start and end date/time must be provided in separate columns.
* '''For field experiments, include the parameters Latitude and Longitude''' in decimal degrees, and the third dimension '''depth''' (e.g. parameters “Depth, sediment, experiment [m]”, "Depth, water, experiment [m]"), even if all observations are from the surface (value = 0). When data are from a depth range, minimum and maximum depths must be provided in separate columns.
* Use "'''Treatment: XY" parameters''', e.g., "Treatment: Temperature, water" to indicate the experimental conditions/treatments for the data.

Experimental data

2026-03-24T14:47:58Z

Awittmann: Remove section numbering because otherwise would be redundant in contents table.

This wiki article describes guidelines on how to prepare experimental data for submission to PANGAEA. Please read our [[Authors Guides]] first which provide general guidelines on how to prepare your metadata and data for publication in PANGAEA. Check if your experimental data file types and format are accepted by PANGAEA (see [[Authors Guides#Data types and file formats accepted by PANGAEA|respective section in our Authors Guides]]). In addition, you can find the template for experimental data in section 2 (coming soon) and the specific requirements for experimental (meta-)data in section 3 below. If you are dealing with biological experimental data, please also have a look at our specific guidelines for [[Biology]].

== Types of experimental data at PANGAEA ==
Experimental data are collected in (semi-)controlled experiments where variables are manipulated (using so-called treatments) to observe their effects e.g. on an organism or environmental sample, in a natural or artificial environment. Experiments are conducted in multiple research domains and diverse experimental set-ups exist. The main types of experiments can be summarized as:

'''a) Field experiments''' are ''in situ'' studies designed to compare the effects of different treatments on organisms or other samples in their natural environment or under conditions that closely resemble it. Conditions are partially controlled and the treatments are set up by researchers, e.g. to investigate the growth of an organism in different microhabitats. This also includes mesocosm studies with an open experimental set-up that is influenced by several external environmental factors.

Example datasets:

* Biodiversity experiment: https://doi.org/10.1594/PANGAEA.967077
* Benthocosm experiment: https://doi.org/10.1594/PANGAEA.974781

'''b) Enclosed outdoor experiments''' are set up outside in a closed experimental system, e.g. greenhouse studies or bottle experiments. External factors are better controlled in these systems and therefore the studied sample or organism is less influenced by external environmental factors than in field studies. Relevant environmental factors for these outdoor experiments may e.g. include the natural daily cycle of light or air temperature.

Example datasets:

* Greenhouse experiment: https://doi.org/10.1594/PANGAEA.973270
* Ex-situ cultivation system & subsequent outdoor bottle incubation: https://doi.pangaea.de/10.1594/PANGAEA.973666

'''c) 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 carbon dioxide (CO2) partial pressure.

Example datasets:

* Culture experiments with phytoplankton: https://doi.org/10.1594/PANGAEA.964086
* Incubation experiments with sediments: https://doi.org/10.1594/PANGAEA.977247
* Laboratory experiments with artificial kelp/simulated water flow: https://doi.pangaea.de/10.1594/PANGAEA.971269

The following data '''are not considered''' experimental data in PANGAEA:
* '''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. to determine the abundance of species in space and time. For the submission of field observation data, have a look at our general and domain-specific templates: [[Best practice manuals and templates]].
* '''Computational experiments''' (e.g. modelling data) are only archived at PANGAEA, if a direct relation to a corresponding environmental study exists. For further details, see our article [[Model data and PANGAEA]].

== General template for experimental data ==
coming soon

== Specific requirements concerning metadata and data ==

=== Metadata - Abstract ===

* For general guidelines, please read: [[Abstract]].
* Describe '''how the experiment was carried out''', and include the '''conditions/treatments before and during''' the experiment.
* Specify the '''type of experiment''' and the '''location''' where the experimental data were collected, e.g. "field experiment in the Wadden Sea at Spiekeroog", or "laboratory experiment at the Marine Biology laboratory at Kiel University".

=== Metadata - Keywords ===
It is '''mandatory to include ONE of the following keywords''' for experimental data to distinguish them from other datasets with field observations in PANGAEA:

* Field experiment
* Laboratory experiment
* Mesocosm experiment
* Greenhouse experiment
* Experiment
Further keywords, such as “ship-based”, “land-based”, the name of the experimental site or the analysed sample/species may be included in addition.

=== Metadata - Event table ===
The Event table (see template, coming soon) gives an overview when, where and how the experimental sample, organism or data was collected. Please provide the following event information:

* '''Event(s) for the actual experiments''' including the location and the start and end date/time of the experiments
* If available, additionally provide the '''original sampling event''' of the studied sample/organism in the field prior to the experiments
For general information regarding the event information, please read: [[Event]]. Please use one of the following methods for the events of the actual experiments: “Field experiment”, “Laboratory experiment”, “Mesocosm experiment”, “Greenhouse experiment”, “Experiment”.

=== Metadata - Parameter table ===
This table summarizes all variables (PANGAEA "[[Parameter|parameters]]") that are included in the data table, specifies units, principal investigator(s) and the methods used to generate the data. Please read our [[Authors Guides#Requirements for the data files and their metadata|general requirements for parameter information]] and see our respective template (coming soon). Specific requirements for experimental data include:

* The parameter name should specify whether the values in a column reflect an '''experimental conditions/treatment''' '''or a measured variable'''. For treatment parameters, use the syntax '''Treatment: XY''', e.g., "Treatment: temperature", “Treatment: light intensity”, or “Treatment: carbon dioxide”.
* The parameter name may include the type of sample or species name, e.g. “Mytilus edulis, wet mass“.

=== Data table/files ===
Prepare your data according to our general requirements for [[Authors Guides#How to prepare tabular Data:|tabular data]] and [[Authors Guides#How to prepare binary files:|binary files]]. Specific requirements for tabular experimental data include:

* The '''first column''' must be the '''Event label'''. The Event label must correspond to the event information of the actual experiments included in the Event table.
* The '''second column''' must be '''"Type of study'''" to separate experimental datasets from field observations. Use e.g. "Laboratory experiment" or "Field experiment" as values, even if all data are from the same type of study.
* If an organism (e.g. Mytilus edulis) was investigated in the experiment, the species should be indicated in the parameter names. Alternatively, if multiple species were studied, include e.g. the '''column "Species, unique identification"''' for the scientific name of the species even if only one species was studied. Please provide a [https://en.wikipedia.org/wiki/LSID Life Science Identifier] (LSID e.g. <nowiki>urn:lsid:marinespecies.org:taxname:140656</nowiki>) in a '''separate column''', e.g. “'''Species, unique identification (Semantic URI)'''”. We recommend to use [https://www.marinespecies.org/index.php WoRMS] LSIDs for marine organisms or [https://www.itis.gov/ Integrated Taxonomic Information System] (ITIS) LSIDs for terrestrial and limnic organisms.
* Any other type of studied samples (e.g. sediment) can either be indicated in the parameter names or alternatively specified in the '''column "Sample type"'''.
* Include the '''date/time of experiment''' in '''ISO-format''' and as '''UTC''' (use e.g. parameter "Sampling date/time, experiment" or "Date/time start, experiment", "Date/time end, experiment"). Start and end date/time must be provided in separate columns.
* '''For field experiments, include the parameters Latitude and Longitude''' in decimal degrees, and the third dimension '''depth''' (e.g. parameters “Depth, sediment, experiment [m]”, "Depth, water, experiment [m]"), even if all observations are from the surface (value = 0). When data are from a depth range, minimum and maximum depths must be provided in separate columns.
* Use "'''Treatment: XY" parameters''', e.g., "Treatment: Temperature, water" to indicate the experimental conditions/treatments for the data.

Experimental data

2026-03-24T14:14:07Z

Awittmann: Corrected typos, reorganized some information, and added required information on taxonomic terms in the data table (according to Biology Wiki article).

This wiki article describes guidelines on how to prepare experimental data for submission to PANGAEA. Please read our [[Authors Guides]] first which provide general guidelines on how to prepare your metadata and data for publication in PANGAEA. Check if your experimental data file types and format are accepted by PANGAEA (see [[Authors Guides#Data types and file formats accepted by PANGAEA|respective section in our Authors Guides]]). In addition, you can find the template for experimental data in section 2 (coming soon) and the specific requirements for experimental (meta-)data in section 3 below. If you are dealing with biological experimental data, please also have a look at our specific guidelines for [[Biology]].

== 1) Types of experimental data at PANGAEA ==
Experimental data are collected in (semi-)controlled experiments where variables are manipulated (using so-called treatments) to observe their effects e.g. on an organism or environmental sample, in a natural or artificial environment. Experiments are conducted in multiple research domains and diverse experimental set-ups exist. The main types of experiments can be summarized as:

'''a) Field experiments''' are ''in situ'' studies designed to compare the effects of different treatments on organisms or other samples in their natural environment or under conditions that closely resemble it. Conditions are partially controlled and the treatments are set up by researchers, e.g. to investigate the growth of an organism in different microhabitats. This also includes mesocosm studies with an open experimental set-up that is influenced by several external environmental factors.

Example datasets:

* Biodiversity experiment: https://doi.org/10.1594/PANGAEA.967077
* Benthocosm experiment: https://doi.org/10.1594/PANGAEA.974781

'''b) Enclosed outdoor experiments''' are set up outside in a closed experimental system, e.g. greenhouse studies or bottle experiments. External factors are better controlled in these systems and therefore the studied sample or organism is less influenced by external environmental factors than in field studies. Relevant environmental factors for these outdoor experiments may e.g. include the natural daily cycle of light or air temperature.

Example datasets:

* Greenhouse experiment: https://doi.org/10.1594/PANGAEA.973270
* Ex-situ cultivation system & subsequent outdoor bottle incubation: https://doi.pangaea.de/10.1594/PANGAEA.973666

'''c) 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 carbon dioxide (CO2) partial pressure.

Example datasets:

* Culture experiments with phytoplankton: https://doi.org/10.1594/PANGAEA.964086
* Incubation experiments with sediments: https://doi.org/10.1594/PANGAEA.977247
* Laboratory experiments with artificial kelp/simulated water flow: https://doi.pangaea.de/10.1594/PANGAEA.971269

The following data '''are not considered''' experimental data in PANGAEA:
* '''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. to determine the abundance of species in space and time. For the submission of field observation data, have a look at our general and domain-specific templates: [[Best practice manuals and templates]].
* '''Computational experiments''' (e.g. modelling data) are only archived at PANGAEA, if a direct relation to a corresponding environmental study exists. For further details, see our article [[Model data and PANGAEA]].

== 2) General template for experimental data ==
coming soon

== 3) Specific requirements concerning metadata and data ==

=== Metadata - Abstract ===

* For general guidelines, please read: [[Abstract]].
* Describe '''how the experiment was carried out''', and include the '''conditions/treatments before and during''' the experiment.
* Specify the '''type of experiment''' and the '''location''' where the experimental data were collected, e.g. "field experiment in the Wadden Sea at Spiekeroog", or "laboratory experiment at the Marine Biology laboratory at Kiel University".

=== Metadata - Keywords ===
It is '''mandatory to include ONE of the following keywords''' for experimental data to distinguish them from other datasets with field observations in PANGAEA:

* Field experiment
* Laboratory experiment
* Mesocosm experiment
* Greenhouse experiment
* Experiment
Further keywords, such as “ship-based”, “land-based”, the name of the experimental site or the analysed sample/species may be included in addition.

=== Metadata - Event table ===
The Event table (see template, coming soon) gives an overview when, where and how the experimental sample, organism or data was collected. Please provide the following event information:

* '''Event(s) for the actual experiments''' including the location and the start and end date/time of the experiments
* If available, additionally provide the '''original sampling event''' of the studied sample/organism in the field prior to the experiments
For general information regarding the event information, please read: [[Event]]. Please use one of the following methods for the events of the actual experiments: “Field experiment”, “Laboratory experiment”, “Mesocosm experiment”, “Greenhouse experiment”, “Experiment”.

=== Metadata - Parameter table ===
This table summarizes all variables (PANGAEA "[[Parameter|parameters]]") that are included in the data table, specifies units, principal investigator(s) and the methods used to generate the data. Please read our [[Authors Guides#Requirements for the data files and their metadata|general requirements for parameter information]] and see our respective template (coming soon). Specific requirements for experimental data include:

* The parameter name should specify whether the values in a column reflect an '''experimental conditions/treatment''' '''or a measured variable'''. For treatment parameters, use the syntax '''Treatment: XY''', e.g., "Treatment: temperature", “Treatment: light intensity”, or “Treatment: carbon dioxide”.
* The parameter name may include the type of sample or species name, e.g. “Mytilus edulis, wet mass“.

=== Data table/files ===
Prepare your data according to our general requirements for [[Authors Guides#How to prepare tabular Data:|tabular data]] and [[Authors Guides#How to prepare binary files:|binary files]]. Specific requirements for tabular experimental data include:

* The '''first column''' must be the '''Event label'''. The Event label must correspond to the event information of the actual experiments included in the Event table.
* The '''second column''' must be '''"Type of study'''" to separate experimental datasets from field observations. Use e.g. "Laboratory experiment" or "Field experiment" as values, even if all data are from the same type of study.
* If an organism (e.g. Mytilus edulis) was investigated in the experiment, the species should be indicated in the parameter names. Alternatively, if multiple species were studied, include e.g. the '''column "Species, unique identification"''' for the scientific name of the species even if only one species was studied. Please provide a [https://en.wikipedia.org/wiki/LSID Life Science Identifier] (LSID e.g. <nowiki>urn:lsid:marinespecies.org:taxname:140656</nowiki>) in a '''separate column''', e.g. “'''Species, unique identification (Semantic URI)'''”. We recommend to use [https://www.marinespecies.org/index.php WoRMS] LSIDs for marine organisms or [https://www.itis.gov/ Integrated Taxonomic Information System] (ITIS) LSIDs for terrestrial and limnic organisms.
* Any other type of studied samples (e.g. sediment) can either be indicated in the parameter names or alternatively specified in the '''column "Sample type"'''.
* Include the '''date/time of experiment''' in '''ISO-format''' and as '''UTC''' (use e.g. parameter "Sampling date/time, experiment" or "Date/time start, experiment", "Date/time end, experiment"). Start and end date/time must be provided in separate columns.
* '''For field experiments, include the parameters Latitude and Longitude''' in decimal degrees, and the third dimension '''depth''' (e.g. parameters “Depth, sediment, experiment [m]”, "Depth, water, experiment [m]"), even if all observations are from the surface (value = 0). When data are from a depth range, minimum and maximum depths must be provided in separate columns.
* Use "'''Treatment: XY" parameters''', e.g., "Treatment: Temperature, water" to indicate the experimental conditions/treatments for the data.

PANGAEA Community Workshops

2026-01-08T11:41:29Z

Awittmann: FAIR data principles: inserted link to GO FAIR website, strand -> course, FAIR standards -> FAIR principles, inserted links to pangaeapy and pangaear, CWS's -> workshops

[[File:PANGAEA Banner CWS&Partner sans.png|thumb|773x773px]]

== About ==
The '''PANGAEA Community Workshop Series (CWS)''' is an established training initiative launched in 2021. It was developed to strengthen research data management (RDM) competences among users of PANGAEA and to promote good scientific practice in the preparation, publication, and reuse of research data. Combining theoretical instruction with practical, hands-on components, the workshop series provides participants with a comprehensive understanding of how to work effectively with the PANGAEA data repository. It is primarily designed for early career scientists but is open for participation by anyone interested.

The overarching goals of the series are to raise awareness of [https://www.go-fair.org/fair-principles/ FAIR data principles] and high-quality data management, empower researchers to make best use of PANGAEA services, and improve the overall efficiency of the data publication process. By educating authors on how to prepare their data appropriately, the workshops not only enhance participants’ individual scientific visibility but also contribute to reducing editorial workload and improving productivity within PANGAEA.

The CWS is a contribution to the [https://www.denbi.de/training de.NBI training network] and covers the two major topics relevant to the use of a data repository.

=== FAIR Data Publications with PANGAEA ===
The course '''“FAIR Data Publications with PANGAEA”''', usually held in November, focuses on the submission and publication aspects of data management. Participants gain detailed insights into how to prepare datasets and metadata for submission, understand editorial procedures, and learn how to ensure their outputs meet FAIR principles. The benefits for researchers are manifold: publishing FAIR data increases citation rates, visibility, and scientific impact, while promoting transparency and encouraging collaboration. Data authors also gain recognition independent of traditional paper authorship, ensuring proper credit for data generation and processing.

=== Finding and Retrieving Data from PANGAEA ===
The second course, '''“Finding and Retrieving Data from PANGAEA”''', is devoted to the discovery and reuse of published data and is usually offered in May. It introduces participants to the repository’s powerful search capabilities, standardized metadata structures, and integration with major data portals such as OpenAIRE, DataCite, and Google Dataset Search. Through practical exercises, attendees learn to efficiently locate, combine, and analyze datasets using standard web protocols and scripting tools like [https://pypi.org/project/pangaeapy/ Python] and [https://github.com/ropensci/pangaear R]. High-quality, harmonized data products curated by domain experts ensure that users can confidently employ PANGAEA data in new studies and analytical workflows, thereby fostering reproducibility, innovation, and cross-disciplinary research.

== Format Details ==
The workshops are conducted '''online via web conference''', allowing participants from around the world to join easily. Each workshop spans '''two days''', typically held on '''Thursday and Friday''', with '''two-hour sessions per day'''. The format is designed to be compact yet interactive, combining presentations with live demonstrations and short exercises. '''No prior experience or prerequisites''' are required—participants of all backgrounds are welcome to attend.

== Upcoming Editions and staying tuned ==
New editions of the '''PANGAEA Community Workshop Series''' are held regularly, typically twice a year, featuring updated content that reflects emerging developments in open science, FAIR data practices, and digital research infrastructures. Researchers interested in participating or staying informed about future events are encouraged to subscribe to the '''PANGAEA Trainings mailing list'''. The list provides timely updates on upcoming workshops and other training activities and materials. You can subscribe to the list [https://lists.pangaea.de/listinfo/training '''here'''].

=== Next Editions ===
The next editions are scheduled for:
{| class="wikitable"
|+
!Date
!Topic
!Registration
|-
|07.-08.05.2026
|Finding and Retrieving Data from PANGAEA
|[https://events.hifis.net/e/CWS2605 Link] (reg. opens April 2026)
|-
|12.-13.11.2026
|FAIR Data Publications with PANGAEA
|[https://events.hifis.net/e/CWS2611 Link] (reg. opens Oct. 2026)
|-
|
|
|
|}

Biology

2025-12-16T09:09:36Z

Awittmann: Updated "Molecular biology" section with respect to ASV Registry and GFBio data submission service and templates.

Please use the templates when preparing your data and first read: [[Authors Guides|Author Guides]]. The following defines frequent data types and summarizes how to prepare biological data collected in the field or laboratory for submission to PANGAEA. Please note the following:
* In addition to the biological data, the georeferenced contextual data such as conductivity, temperature and depth data ([[CTD Underway Data|CTD]]), pH value, humidity, etc. should also be submitted to and archived at PANGAEA. If these data are archived and available in open access somewhere else, please provide the DOI link in the references box of the web submission form.
* The PANGAEA record should be understandable in itself, i.e. a potential user of the data should be able to judge quality and suitability for reuse. Thus, the record should be rich in metadata.
* The title(s), [[Abstract|abstract]](s) and keywords will need to be pasted into the web interface.
* For a complete data submission, upload all of the three tables included in the templates, i.e. the events, parameters and data tables.

== Data types and templates ==

=== Field observations/biodiversity ===

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.

'''Examples:'''
* https://doi.org/10.1594/PANGAEA.946885
* https://doi.org/10.1594/PANGAEA.950504

'''Templates with further instructions:'''

[[Media:Envir sample template bio.xlsx|Spreadsheet template]] ('''xlsx file''')

[[Media:Envir sample template bio tsv.zip|Textfile template]] ('''zipped tab separated text files'''. Please see instruction file 0_README.md first!)

=== Field experiments (including e.g. mesocosm studies) ===

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.

'''Example:'''

* https://doi.pangaea.de/10.1594/PANGAEA.959575

'''Template with further instructions:'''

[[Media:Field exp template.xlsx|Spreadsheet template]] ('''xlsx file''')

=== Laboratory experiments (including e.g. ship-based experiments) ===

Laboratory experiments are (comparative) studies on organisms under controlled conditions set up in a land-based or ship-based laboratory. E.g. behaviour of fish larvae in response to different treatments of CO2 partial pressure.

'''Examples:'''
* https://doi.pangaea.de/10.1594/PANGAEA.957929
* https://doi.pangaea.de/10.1594/PANGAEA.959614
* https://doi.org/10.1594/PANGAEA.951078

'''Template with further instructions:'''

[[Media:Lab exp template.xlsx|Spreadsheet template]] ('''xlsx file''')

=== Molecular biology ===

PANGAEA does not archive molecular sequence data, but will accept related (meta)data and establish links to the [https://www.ebi.ac.uk/ena/browser/about European Nucleotide Archive] (ENA). For metabarcoding data resulting in ASV/OTU counts and their taxonomic annotations, we recommend to conribute to the [https://data.bolgermany.de/gbol1/metabarcoding ASV Registry] of the German Barcode of Life or similar services in your home country. Both raw sequence reads and ASV/OTU tables can be submitted via the [https://submissions.gfbio.org/ GFBio data submission service] using the respective [https://kb.gfbio.org/display/KB/Data+Submission+Templates templates].

For more information, please read: [[Molecular data in PANGAEA]].

Examples with links to accession numbers:
* https://doi.org/10.1594/PANGAEA.923271
* https://doi.org/10.1594/PANGAEA.935870

== Metadata and Data ==

=== Metadata – [[Abstract]] ===
*The abstract/description of a dataset is NOT identical to the manuscript/article abstract, please read: [[Abstract]].
*Each submitted data table requires one specific title and abstract, even if data tables are organized in a [[PANGAEA publication types|Bundled publication]] with a parent record.
*Specify whether data were collected during a field campaign, a field experiment or a land-based or ship-based laboratory experiment.
* Depending on the data type, include the following information in the abstract:
{| class="wikitable"
|+
|-
!Data type!!Additional information in abstract
|-
|Data collected directly in the field ||> Characterization of conditions in the field
|-
|Experimental data from an ''in situ''/field study ||
> Experiment site

> Conditions before and during the experiment
|-
|Laboratory experiments on cultured organisms||
> Name of the laboratory

> Name of the culture(s) collection

> Time of cultivation and no. of generations before the experiment

> Culture conditions before and during the experiment
|-
|Laboratory experiments on field-collected organisms
|
> Collection site

> Name of the laboratory

> Place, time and conditions of cultivation/animal keeping before the experiment

> Culture conditions during the experiment
|}
=== Metadata – Keywords ===

Include suitable keywords, such as:
* “Laboratory experiment” ('''mandatory''' for laboratory experiments)
* “Field experiment” ('''mandatory''' for field experiments)
* “Mesocosm experiment”
* “Field observation”
* “Cultured organism”
* “Field-collected organism”
* “Ship-based”
* “Land-based”
* “Mobile laboratory”
* Collection/experiment site
* Name of laboratory or ship

=== Metadata – [[Event|Events]] table ===

This Event table gives an overview of the when, where and how a sample or (experimental) organism was collected (prior to the experiment in case of laboratory studies), please see the [[Media:Envir sample template bio.xlsx|template]] and read: [[Event]].
* Event label, unique identifier of sampling time and location.
* Campaign, e.g. ship cruise ID, please read: [[Campaign]].
* Device or method used to collect a sample or (experimental) organism, please read: [[Method]].
* For field experiments: Device is e.g. “Field experiment” or “Mesocosm experiment (MESO)”.
* Date and time in ISO-format (e.g. 1954-04-07T13:34:11) as coordinated universal time (UTC), start and end date/time must be provided in separate columns.
* Latitude and longitude in decimal degrees (S and W are negative) of sample/organism collection site or field experiment site. For transects, start and end latitude and longitude must be provided in separate columns.
* Elevation (altitude, sea bottom depth, negative below sea level) is optional. For transects, start and end elevation must be provided in separate columns.

=== Metadata – Parameter table ===

This table summarizes all variables (PANGAEA "[[parameter|Parameters]]") that are included in the data table, specifies units, principal investigator(s) and the methods used to generate the data, please see the [[Media:Envir sample template bio.xlsx|template]]
* '''Parameter''' name of the measured or determined characteristic needs to be given in full, not as abbreviation.
* The parameter name may include the species name, e.g. “Mytilus edulis, wet mass“.
* The parameter name should specify whether a parameter reflects the experimental conditions/treatment or the measured variable. For treatment parameters, use the syntax "Treatment: XY" parameters, e.g., "Treatment: temperature".
* '''Unit''', SI units are preferred
* '''Principal investigator''', i.e. the person responsible for the collected data, can be different for each parameter.
* Information about the '''method/devices''' used, e.g. "Conductivity meter, Mettler Toledo, SevenGo pro SG7". If no instrument is available: provide the method used to measure the parameter, e.g. "14C radioactive tracer incubation according to Zhuang et al. 2018, doi:10.1111/1462-2920.14406". Each parameter/data set column can be assigned a separate method/device. For further information on PANGAEA method/devices, see [https://wiki.pangaea.de/wiki/Method here]
* [https://www.pangaea.de/lists/parameter/all-byname Current list of parameters used in PANGAEA]

=== Data table ===

* Only one (1) variable (PANGAEA "[[parameter|parameter]]") per column, please see the [[Media:Envir sample template.xlsx|template]].
* The column header contains the full parameter name and unit in squared brackets.
* If data are missing, leave the cell empty (do NOT enter "NA" or "-" etc.).
* Abbreviations should be avoided or need to be explained.
* Event label (always first column) must correspond to the entries in the events table, see [[Event]].
* Experimental data must contain parameter "Type of study" (always second column). Enter "Laboratory experiment" or "Field experiment" as values, even if all data are from the same type of study.
* Include date/time of observation if they differ from time given in the Event (use parameters "Date/time" or "Date/time start", "Date/time end"). For experiments, include date/time of experiment (use parameters "Sampling date/time, experiment" or "Date/time start, experiment", "Date/time end, experiment). Start and end date/time must be provided in separate columns
* For field observations and field experiments, include latitude and longitude. For transects, start and end latitude and longitude must be provided in separate columns.
* For field observations and field experiments, depth should be included (e.g. parameters “Depth, water”, “Depth, sediment”, "Depth, water, experiment"), even if all observations are from the surface (value = 0) as these parameters also define medium in which the samples were taken. When data are from a depth range, minimum and maximum depths must be provided in separate columns.
* To indicate whether a variable represents adjusted/intended values rather than a measured value, use "Treatment: XY" parameters, e.g., "Treatment: Temperature, water".
* For experiments, you may use the experiment parameters “Time of organism in laboratory”, “Name of laboratory”, "Latitude, experiment", "Longitude, experiment"
* For studies on cultured organisms include “Culture location”, “Name of culture collection” and “Uniform resource locator/link to reference” for a link to the culture collection.
* Spell-check all [[taxon]]<nowiki/>omic terms, e.g. by using the taxon match tools by the World Register of Marine Species ([http://www.marinespecies.org/aphia.php?p=match WoRMS]) or [https://www.lifewatch.be/data-services/ LifeWatch].
* For taxonomic terms in the data matrix, include e.g. the column "Species, unique identification" for the scientific name of the species even if only one species was studied. Please provide a [https://en.wikipedia.org/wiki/LSID Life Science Identifier] (LSID e.g. <nowiki>urn:lsid:marinespecies.org:taxname:140656</nowiki>) in a separate column, e.g. “Species, unique identification (Semantic URI)”. We recommend to use [https://www.marinespecies.org/index.php WoRMS] LSIDs for marine organisms or [https://www.itis.gov/ Integrated Taxonomic Information System] (ITIS) LSIDs for terrestrial and limnic organisms.
* For a link to e.g. [[Molecular data in PANGAEA|genetic data]], include the column "Accession number, genetics", and enter e.g. NCBI/ENA accession numbers as values.

== Frequently asked questions ==

=== Laboratory experiments ===
'''Do I need to provide georeferences for the sampling site of organisms that have been cultured or bred in the laboratory for many generations?'''

Yes, we encourage you to provide as much detail as possible on the origin of the organisms used in your laboratory study, especially if your study is relevant to the environmental sciences. Reproducibility of results depends on the laboratory strain used and the study location. The more (exact and structured) information we provide, the easier it is to decide on the suitability for reuse of the data. Please provide an events table as part of your submission. However, we are aware that for some laboratory model organisms it is close to impossible to track down the sampling event. In this case the strain(s) and culturing conditions need to be clearly described in the abstract.

Provide exact georeferences for the origin of laboratory strains in the events table and give details on strain(s) and culturing conditions in the abstract for studies like this:

* Gebühr, C., Sheward, R. M., Herrle, J. O., & Bollmann, J. (2021). Strain-specific morphological response of the dominant calcifying phytoplankton species ''Emiliania huxleyi'' to salinity change. ''PloS one'', ''16''(2), e0246745. https://doi.org/10.1371/journal.pone.0246745

Include details on strain(s) and breeding conditions in the abstract for studies like this:

* von Kortzfleisch, V. T., Karp, N. A., Palme, R., Kaiser, S., Sachser, N., & Richter, S. H. (2020). Improving reproducibility in animal research by splitting the study population into several 'mini-experiments'. ''Scientific reports'', ''10''(1), 16579. https://doi.org/10.1038/s41598-020-73503-4

Abstract

2025-05-08T13:53:18Z

Awittmann: Corrected typo

For each [[dataset|dataset]] published in PANGAEA, the abstract provides a concise and method-oriented description of the observation or measurement, namely what, when, where, why and how the data was collected. The summary should consist of meaningful running text. The format of the dataset abstract is the same as that of paper abstracts.

For data submissions with single data tables, the abstract should be inserted into the abstract section of the submission form. The length should be ideally limited to 5000 characters. '''If a submission contains several data sets (tables), an individual abstract must be provided for each data set'''. Dataset specific abstracts can be similar to one another, but should contain at least one sentence that specifically relates to content of the respective data table.

==Information that an abstract should contain==
* '''WHAT''' are the observations made, what parameters were measured (especially if you publish data in files such as netCDF, or other proprietary formats), what samples were collected, what experiments were performed, what was modeled?
* '''WHEN''' was the data collected (time of the measurement not the campaign)? What is the temporal coverage? The precision of is information coverage should be made in context of the temporal extent of the dataset, e.g. geological era, centuries, millennia, decades, months, days, ...
* '''WHERE''' was the data collection done (e.g. Drake passage), what is the geographical coverage? The precision of this information should be made in context of the spatial extent of the dataset, e.g.: global, sea, ocean, continent, country, region, ...
* '''WHY''' was the data collected? What was the purpose? This will have important implications for reusability of the data, and its possible limitations for other purposes.
* '''HOW''' was the data collected? Which devices or methods were used to collect the data? During which campaign or cruise were the data collected?
* '''Abstract may contain necessary references'''. If you include a reference, provide the article DOI or a full citation (if no DOI is available). References relevant to the dataset do not need to appear in the abstract, but can also be linked to the data independently of the abstract (provide the details to the data editor).

==What to avoid==
* Avoid the '''interpretation of results'''.
* Avoid '''acronyms and abbreviations'''; if you use them, first spell them out.
* '''Do not simply copy & paste manuscript abstracts''' or cruise report extracts. Abstracts need to be dataset specific and unique.
* Many '''metadata do not have to be part of the abstract''' because they are already listed in the [[metaheader]] of the published dataset. Like that, they are both human and machine readable. Examples are:
** Contact information of the PI (is listed in the Parameter table of the dataset)
** Link to the cruise report, chief scientist (is part of the [[Event]] information in the dataset or can be added as a reference)
** Exact geolocation (is part of the [[Event]] information in the dataset)
** Title and citation of the related article (article is added as a reference)

==Data collection abstract==
Data [[PANGAEA publication types|collections]] require a common abstract. In addition to that, each of the individual datasets may have a separate abstract.

==Examples==
* A dataset with an informative abstract: {{doi|10.1594/PANGAEA.907748}}
* Abstract for a data collection: {{doi|10.1594/PANGAEA.911261}}
* Abstract for a data collection with additional abstracts for individual data sets: {{doi|10.1594/PANGAEA.908837}}

Biology

2025-05-08T10:14:57Z

Awittmann: update -> Data submission -> author guides

Please use the templates when preparing your data and first read: [[Authors Guides|Author Guides]]. The following defines frequent data types and summarizes how to prepare biological data collected in the field or laboratory for submission to PANGAEA. Please note the following:
* In addition to the biological data, the georeferenced contextual data such as conductivity, temperature and depth data ([[CTD Underway Data|CTD]]), pH value, humidity, etc. should also be submitted to and archived at PANGAEA. If these data are archived and available in open access somewhere else, please provide the DOI link in the references box of the web submission form.
* The PANGAEA record should be understandable in itself, i.e. a potential user of the data should be able to judge quality and suitability for reuse. Thus, the record should be rich in metadata.
* The title(s), [[Abstract|abstract]](s) and keywords will need to be pasted into the web interface.
* For a complete data submission, upload all of the three tables included in the templates, i.e. the events, parameters and data tables.

== Data types and templates ==

=== Field observations/biodiversity ===

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.

'''Examples:'''
* https://doi.org/10.1594/PANGAEA.946885
* https://doi.org/10.1594/PANGAEA.950504

'''Templates with further instructions:'''

[[Media:Envir sample template bio.xlsx|Spreadsheet template]] ('''xlsx file''')

[[Media:Envir sample template bio tsv.zip|Textfile template]] ('''zipped tab separated text files'''. Please see instruction file 0_README.md first!)

=== Field experiments (including e.g. mesocosm studies) ===

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.

'''Example:'''

* https://doi.pangaea.de/10.1594/PANGAEA.959575

'''Template with further instructions:'''

[https://store.pangaea.de/documentation/PANGAEA-Wiki/Templates/Field_exp_template_230626.xlsx Template] (xlsx file)

=== Laboratory experiments (including e.g. ship-based experiments) ===

Laboratory experiments are (comparative) studies on organisms under controlled conditions set up in a land-based or ship-based laboratory. E.g. behaviour of fish larvae in response to different treatments of CO2 partial pressure.

'''Examples:'''
* https://doi.pangaea.de/10.1594/PANGAEA.957929
* https://doi.pangaea.de/10.1594/PANGAEA.959614
* https://doi.org/10.1594/PANGAEA.951078

'''Template with further instructions:'''

[https://store.pangaea.de/documentation/PANGAEA-Wiki/Templates/Lab_exp_template_230626.xlsx Template] (xlsx file)

=== Molecular biology ===

PANGAEA does not archive molecular sequence data, but will accept related (meta)data and establish links to the [https://www.ebi.ac.uk/ena/browser/about European Nucleotide Archive] (ENA). For more information, please read: [[Molecular data in PANGAEA]].

Examples with links to accession numbers:
* https://doi.org/10.1594/PANGAEA.923271
* https://doi.org/10.1594/PANGAEA.935870

== Metadata and Data ==

=== Metadata – [[Abstract]] ===
*The abstract/description of a dataset is NOT identical to the manuscript/article abstract, please read: [[Abstract]].
*Each submitted data table requires one specific title and abstract, even if data tables are organized in a [[PANGAEA publication types|Bundled publication]] with a parent record.
*Specify whether data were collected during a field campaign, a field experiment or a land-based or ship-based laboratory experiment.
* Depending on the data type, include the following information in the abstract:
{| class="wikitable"
|+
|-
!Data type!!Additional information in abstract
|-
|Data collected directly in the field ||> Characterization of conditions in the field
|-
|Experimental data from an ''in situ''/field study ||
> Experiment site

> Conditions before and during the experiment
|-
|Laboratory experiments on cultured organisms||
> Name of the laboratory

> Name of the culture(s) collection

> Time of cultivation and no. of generations before the experiment

> Culture conditions before and during the experiment
|-
|Laboratory experiments on field-collected organisms
|
> Collection site

> Name of the laboratory

> Place, time and conditions of cultivation/animal keeping before the experiment

> Culture conditions during the experiment
|}
=== Metadata – Keywords ===

Include suitable keywords, such as:
* “Laboratory experiment” ('''mandatory''' for laboratory experiments)
* “Field experiment” ('''mandatory''' for field experiments)
* “Mesocosm experiment”
* “Field observation”
* “Cultured organism”
* “Field-collected organism”
* “Ship-based”
* “Land-based”
* “Mobile laboratory”
* Collection/experiment site
* Name of laboratory or ship

=== Metadata – [[Event|Events]] table ===

This Event table gives an overview of the when, where and how a sample or (experimental) organism was collected (prior to the experiment in case of laboratory studies), please see the [[Media:Envir sample template bio.xlsx|template]] and read: [[Event]].
* Event label, unique identifier of sampling time and location.
* Campaign, e.g. ship cruise ID, please read: [[Campaign]].
* Device or method used to collect a sample or (experimental) organism, please read: [[Method]].
* For field experiments: Device is e.g. “Field experiment” or “Mesocosm experiment (MESO)”.
* Date and time in ISO-format (e.g. 1954-04-07T13:34:11) as coordinated universal time (UTC), start and end date/time must be provided in separate columns.
* Latitude and longitude in decimal degrees (S and W are negative) of sample/organism collection site or field experiment site. For transects, start and end latitude and longitude must be provided in separate columns.
* Elevation (altitude, sea bottom depth, negative below sea level) is optional. For transects, start and end elevation must be provided in separate columns.

=== Metadata – Parameter table ===

This table summarizes all variables (PANGAEA "[[parameter|Parameters]]") that are included in the data table, specifies units, principal investigator(s) and the methods used to generate the data, please see the [[Media:Envir sample template bio.xlsx|template]]
* '''Parameter''' name of the measured or determined characteristic needs to be given in full, not as abbreviation.
* The parameter name may include the species name, e.g. “Mytilus edulis, wet mass“.
* The parameter name should specify whether a parameter reflects the experimental conditions/treatment or the measured variable. For treatment parameters, use the syntax "Treatment: XY" parameters, e.g., "Treatment: temperature".
* '''Unit''', SI units are preferred
* '''Principal investigator''', i.e. the person responsible for the collected data, can be different for each parameter.
* Information about the '''method/devices''' used, e.g. "Conductivity meter, Mettler Toledo, SevenGo pro SG7". If no instrument is available: provide the method used to measure the parameter, e.g. "14C radioactive tracer incubation according to Zhuang et al. 2018, doi:10.1111/1462-2920.14406". Each parameter/data set column can be assigned a separate method/device. For further information on PANGAEA method/devices, see [https://wiki.pangaea.de/wiki/Method here]
* [https://www.pangaea.de/lists/parameter/all-byname Current list of parameters used in PANGAEA]

=== Data table ===

* Only one (1) variable (PANGAEA "[[parameter|parameter]]") per column, please see the [[Media:Envir sample template.xlsx|template]].
* The column header contains the full parameter name and unit in squared brackets.
* If data are missing, leave the cell empty (do NOT enter "NA" or "-" etc.).
* Abbreviations should be avoided or need to be explained.
* Event label (always first column) must correspond to the entries in the events table, see [[Event]].
* Experimental data must contain parameter "Type of study" (always second column). Enter "Laboratory experiment" or "Field experiment" as values, even if all data are from the same type of study.
* Include date/time of observation if they differ from time given in the Event (use parameters "Date/time" or "Date/time start", "Date/time end"). For experiments, include date/time of experiment (use parameters "Sampling date/time, experiment" or "Date/time start, experiment", "Date/time end, experiment). Start and end date/time must be provided in separate columns
* For field observations and field experiments, include latitude and longitude. For transects, start and end latitude and longitude must be provided in separate columns.
* For field observations and field experiments, depth should be included (e.g. parameters “Depth, water”, “Depth, sediment”, "Depth, water, experiment"), even if all observations are from the surface (value = 0) as these parameters also define medium in which the samples were taken. When data are from a depth range, minimum and maximum depths must be provided in separate columns.
* To indicate whether a variable represents adjusted/intended values rather than a measured value, use "Treatment: XY" parameters, e.g., "Treatment: Temperature, water".
* For experiments, you may use the experiment parameters “Time of organism in laboratory”, “Name of laboratory”, "Latitude, experiment", "Longitude, experiment"
* For studies on cultured organisms include “Culture location”, “Name of culture collection” and “Uniform resource locator/link to reference” for a link to the culture collection.
* Spell-check all [[taxon]]<nowiki/>omic terms, e.g. by using the taxon match tools by the World Register of Marine Species ([http://www.marinespecies.org/aphia.php?p=match WoRMS]) or [https://www.lifewatch.be/data-services/ LifeWatch].
* For taxonomic terms in the data matrix, include e.g. the column "Species, unique identification" for the scientific name of the species even if only one species was studied. Please provide a [https://en.wikipedia.org/wiki/LSID Life Science Identifier] (LSID e.g. <nowiki>urn:lsid:marinespecies.org:taxname:140656</nowiki>) in a separate column, e.g. “Species, unique identification (Semantic URI)”. We recommend to use [https://www.marinespecies.org/index.php WoRMS] LSIDs for marine organisms or [https://www.itis.gov/ Integrated Taxonomic Information System] (ITIS) LSIDs for terrestrial and limnic organisms.
* For a link to e.g. [[Molecular data in PANGAEA|genetic data]], include the column "Accession number, genetics", and enter e.g. NCBI/ENA accession numbers as values.

== Frequently asked questions ==

=== Laboratory experiments ===
'''Do I need to provide georeferences for the sampling site of organisms that have been cultured or bred in the laboratory for many generations?'''

Yes, we encourage you to provide as much detail as possible on the origin of the organisms used in your laboratory study, especially if your study is relevant to the environmental sciences. Reproducibility of results depends on the laboratory strain used and the study location. The more (exact and structured) information we provide, the easier it is to decide on the suitability for reuse of the data. Please provide an events table as part of your submission. However, we are aware that for some laboratory model organisms it is close to impossible to track down the sampling event. In this case the strain(s) and culturing conditions need to be clearly described in the abstract.

Provide exact georeferences for the origin of laboratory strains in the events table and give details on strain(s) and culturing conditions in the abstract for studies like this:

* Gebühr, C., Sheward, R. M., Herrle, J. O., & Bollmann, J. (2021). Strain-specific morphological response of the dominant calcifying phytoplankton species ''Emiliania huxleyi'' to salinity change. ''PloS one'', ''16''(2), e0246745. https://doi.org/10.1371/journal.pone.0246745

Include details on strain(s) and breeding conditions in the abstract for studies like this:

* von Kortzfleisch, V. T., Karp, N. A., Palme, R., Kaiser, S., Sachser, N., & Richter, S. H. (2020). Improving reproducibility in animal research by splitting the study population into several 'mini-experiments'. ''Scientific reports'', ''10''(1), 16579. https://doi.org/10.1038/s41598-020-73503-4

Authors Guides

2025-03-18T10:01:46Z

Awittmann: In section "How to prepare binary files" I linked to Wiki page "Binary objects" and added maximum file size of 15 GB.

These guides provide essential information for data submitters and authors on how to prepare and submit their data for publication with PANGAEA. We recommend that you read the following information carefully before submitting data to us. These instructions includes the scope of PANGAEA, editorial criteria and processes, and preparation guides for metadata and data.

=I. Mission and Scope=

The information system PANGAEA is operated as an Open Access library aimed at archiving, publishing and distributing georeferenced data from earth and environmental science, compliant to our [https://www.pangaea.de/about/terms.php Terms of Use]. PANGAEA guarantees long-term availability of its content for at least 10 years (~75% is actually older than that). PANGAEA is open to any project, institution, or individual scientist to archive and publish research data.

PANGAEA focuses on georeferenced observational and experimental research data. Citability, comprehensive metadata descriptions, interoperability of data and metadata, a high degree of structural and semantic harmonization of the data inventory as well as the long-term commitment of the hosting institutions (AWI & MARUM) ensures the FAIRness ([https://doi.org/10.1038/sdata.2016.18 Wilkinson et al., 2016]) of archived data both for use by humans and machines (i.e. tools and scripts, federated infrastructures, data portals and aggregators etc.).

Most of the data published on PANGAEA are freely available and can be used under the terms of the license mentioned on the dataset description. A few password-protected datasets are under moratorium due to ongoing projects. The metadata for all published datasets is always open-access under the [https://creativecommons.org/share-your-work/cclicenses/ CC0 license] and includes the Principal Investigator (PI) who can be contacted for individual access.

Each dataset can be identified, shared, published and cited by the [[Citation|data citation]], which includes a Digital Object Identifier ([https://www.doi.org/index.html DOI]). PANGAEA also allows data to be published as supplements to science articles (example) or as citable data collections in combination with data journals such as Nature Scientific Data, Geoscience Data Journal, Earth System Science Data and others.

The PANGAEA data editorial ensures the integrity and authenticity as well as a high usability of your data. Archived data are machine readable and mirrored into our [[Data_warehouse|Data Warehouse]] which allows efficient compilations of data.

If you find PANGAEA useful for your work, please help us in maintaining our service by citing:

'''Felden, Janine; Möller, Lars; Schindler, Uwe; Huber, Robert; Schumacher, Stefanie; Koppe, Roland; Diepenbroek, Michael; Glöckner, Frank Oliver (2023)''': PANGAEA - Data Publisher for Earth & Environmental Science. Sci Data 10, 347 (2023). https://doi.org/10.1038/s41597-023-02269-x

=II. Editorial Criteria and Processes=

==General Information==
PANGAEA is committed to publishing high quality datasets in maximum compliance with the FAIR Data Principles. During the publication process, data and metadata are checked for completeness and plausibility, and are structurally harmonized. This harmonization and standardization promotes a high degree of reusability and interoperability of the data stock and, among other things, supports the optimal readability and further processability of the data by machines and algorithms ([https://doi.org/10.1038/s41597-023-02269-x Felden et al., 2023]). Following standardized procedures, the PANGAEA Editorial Team systematically reviews incoming data submissions and decides whether the submissions are sufficiently mature and of the appropriate quality to be published with PANGAEA. Data submissions that do not meet the scope and/or our quality requirements will be rejected.

Before submitting data to us, please check if there is a community-specific certified FAIR-data-repository for your data type. Community-specific data repositories may be able to better describe, represent and publish your type of data, or bring your data into a discipline-specific context. The repository search platform [https://www.re3data.org re3data] may be very helpful in this regard.

===Data types and file formats accepted by PANGAEA===
PANGAEA publishes primary/validated data from many fields of Earth and Environmental Science as well as Biodiversity research. This includes georeferenced observational (example: https://doi.pangaea.de/10.1594/PANGAEA.967645) and experimental data (example: https://doi.org/10.1594/PANGAEA.966520). PANGAEA is specialized in field observation and experimental data in two-dimensional tabular format with parameters/variables measured provided in columns.

Preferred formats for data are TAB-delimited text files in UTF-8 encoding, or (open) spreadsheet file formats (MS Excel .xlsx, OpenOffice & LibreOffice Calc .ods etc. - please see [[Format|the corresponding wiki article]] for more information). Example: https://doi.org/10.1594/PANGAEA.937808. Tables are not accepted as proprietary or encapsulated file types (e.g., Matlab files .mat or PDF files).

Binary objects such as NetCDF files, seismic data files (e.g. segy), photos/images and videos are also accepted as long as they are fully described with metadata. In order to follow the FAIR data principles and guarantee reusability for PANGAEA data publications, all such binary files must be usable with open source software. Example: https://doi.org/10.1594/PANGAEA.936185

As an addition to numerical (or binary) data, supporting documentation on datasets can be archived and published (e.g. processing reports, instrument calibration protocols, standard operating procedures). These can be submitted as PDF/A, plain text or open document formats like RTF, ODF or MS Office documents (.docx, .xlsx). Links to such documentation already published elsewhere are also possible. In this case, please provide a complete reference.

=== Data types and formats PANGAEA does not accept (i.a. no longer) ===

'''Raw Data''': Raw data without metadata ([[Processing levels|Processing level]] 0) are not accepted in PANGAEA. Raw data with their metadata (Processing level 1) may be accepted under certain circumstances and should be accompanied with their primary/validated data.

'''Sequence data''': PANGAEA does not archive molecular sequence data, but will accept related (meta)data and create cross-links to, e.g., the [https://www.ebi.ac.uk/ena/browser/about European Nucleotide Archive] (ENA). For more information, please read: [[Molecular data in PANGAEA]]. If your molecular data are accompanied by environmental parameters, we recommend that you submit your data to [https://www.gfbio.org/ GFBio's] free and [https://submissions.gfbio.org/ multidisciplinary publication service].

'''Model data''': Many, but not all, types of model and simulation data will no longer be accepted for publication. Please read more about our definitions, explanations and restrictions in our corresponding Wiki article "[[Model data and PANGAEA]]". Data outputs from models that are entirely based on algorithms and (process) generalizations and do not have a concrete (and clearly specifiable) spatial reference to field observations, will not be accepted by PANGAEA. For climate modeling/simulation data, the World Data Center for Climate (WDCC), operated by the German Climate Computing Center ([https://www.dkrz.de/en/services/data-publication DKRZ]), provides an established long-term archiving and publication service.

'''Software/Code''': PANGAEA is not a suitable platform to publish software. In general, we recommend storing and managing software products or any kind of scripts and code on specialized platforms such as [https://github.com/ GitHub] in combination with versioned publishing in e.g. [https://zenodo.org Zenodo]. Zenodo provides persistant identifiers which can be cross-linked to your dataset published in PANGAEA. This is the preferred method to combine PANGAEA datasets and relevant versions of code.

'''Other formats''': Data presented exclusively as plots/figures, standalone PDF or MS Word documents will not be published. Tables in device-specific (e.g. CTD sensor output) or proprietary formats such as Matlab .mat files and [https://cran.r-project.org/ R-files] or other program-specific formats will not be accepted for publication. The same applies to topic/community-specific formats, which cannot be reused with open source software. These file types require transformation into accepted file formats (see our wiki article [[Format|Data types and formats]]).

===Usual turn-over times, timelines and publishing options===

Depending on the extent and complexity of your data submission the editorial process and minting of DOI names for submissions, not affiliated with our hosting institutions MARUM or AWI, to project and institutional partners (our front offices) may take up to several months. Temporary access keys for journal reviewers can be provided once our (initial formal and subsequent in-depth) review stages have been completed and the data have been successfully ingested into the PANGAEA system. Usually this takes 6-8 weeks after the initial acceptance of the submission for publication. A data citation including the DOI is created at the very end of the curation workflow. Therefore, we strongly recommend submitting data as early as possible so that the respective citation and DOI can be generated in time to be included in your scholarly publications. To gain higher processing priority, PANGAEA is open to project- and institutional cooperations including human ressources.

Regarding (optional) associated moratoria and updates to data during the paper publication process, we offer several options for data publications:
{| class="wikitable"
|+ Dataset option for moratorium and open access
|-
! No !! Dataset options !! Status !! DOI
|-
| 1 || In review & access restricted || Dataset is open for corrections, citation is preliminary, metadata are available to the public, data not available to the public (e.g. during article review) || DOI not registered, changes/updates in metadata and data possible
|-
| 2 || In review & no access restriction || Dataset is open for corrections, citation is preliminary, metadata and data already available to the public (e.g. public review) || DOI not registered, changes/updates in metadata and data possible
|-
| 3 || Published & access restricted || Dataset is final and fully citable, metadata are available to the public, data not yet available to the public (moratorium) || DOI registered, no more changes except for information regarding your paper publication
|-
| 4 || Published & no access restriction || Dataset is final and fully citable, metadata and data are open access under the CC0 and CC-BY license, respectively || DOI registered, no more changes except for information regarding your paper publication
|}

==The editorial process==

[[File:Workflow.png|600px|thumb|right|Workflow overview of a data publication]]

The '''workflow''' for a [[data publication]] from source to publication is similar to the process established in the scientific literature (submission > review > editing > publication). The editorial process follows a two-step review procedure and is coordinated by the Editor-in-Chief and our Data [[Editor]]s. The workflow and communication of each data submission is documented and tracked through our ticket system.

The workflow is an interaction between the (corresponding) author and the editorial team and consists of 8 steps:
# '''Data submission''' - Authors submit their dataset and a contextual description of their dataset ([[metadata]]) using the [https://www.pangaea.de/submit/ submission online form]. They follow the guidelines provided in this document and, if necessary, project or institution specific data policies.
# '''Initial review''' - Editorial staff will review the submission to determine acceptance for further evaluation. Consultation with our expert editors may be part of this decision. The main focus of this review stage is to assess the scope and significance of the data submitted for publication with PANGAEA, to evaluate the data submission for completeness of metadata, and to assess the validity and format of the data provided. If the necessary requirements are not met, a reminder will be sent to the author.
# '''Acceptance/Rejection''' - Once the submission is considered complete and the dataset is accepted for publication in PANGAEA, the author will be notified via the ticket system and associated emails. If the submission does not meet the requirements of PANGAEA, it will be rejected. In this case, the author will be informed.
# '''Editorial Review''' - Once the submission is due for processing, it is assigned to an expert data editor. The editor thoroughly reviews the metadata and data for validity and plausibility. The editor will contact the author, if there are open questions about the submission. Please note: If the data and metadata do not meet PANGAEA's quality standards or the submitting author does not respond to the editors’ requests, the submission may be rejected.
# '''Processing/Data import''' - Data and metadata are prepared for import into the relational database, or for file archiving on our servers. During this process, the metadata and data are structurally harmonized and aligned with standardized terminologies. Submitted data can be reformatted by the editor to comply with the PANGAEA [[data model]]. This step may involve transposing, merging or splitting tables, adding metadata columns (such as official [[event]] labels and [[Geocode|geocodes]]), etc.. After import, the editor performs a final check of the dataset.
# '''Dataset proof''' - The editor sends a temporary link of the dataset landing page to the author(s) and asks for a proofread. The [[DOI]] is assigned, but not yet registered ("activated"). The dataset [[status]] is set to "in review" and data remains password protected at this stage (option #1 in the table above). Associated metadata is always open access (CC0 license).
# '''Corrections''' - Through an iterative process between author and editor, the dataset is edited until the final '''approval by the author'''.
# '''Publication''' - The dataset [[Status|status]] is set to "published"; the DOI will be activated four weeks after the final edits and will then be part of the official dataset [[Citation|citation]]. At the author's request, [[Password|password protection]] may be maintained (or set up) for a period of up a maximum of two years (option #3). Otherwise metadata and data are open access under the respective license (option #4). In case the dataset is under moratorium a temporary access link with an expiration date can be provided at the request of the author, e.g. to share the data with individuals or groups, such as co-authors or anonymous reviewers.

== Costs ==
Basic operations are covered by institutional and public funding, but in order to ensure high quality processing and archiving of new data, PANGAEA requires additional funding. In the case that the data are submitted as part of a project with funding available for publication costs (e.g. as part of the costs for [https://www.dfg.de/formulare/52_01/52_01_en.pdf Open Access publications at the DFG]), PANGAEA would appreciate a financial contribution of 500.– € (net) per data submission. Other forms of funded collaborations are highly appreciated (e.g. as project partner). Please [https://www.pangaea.de/contact/ contact us] for further information.

= III. Guidelines for data submission and formatting =
This chapter describes how to prepare your metadata and data for submission to PANGAEA. We recommend that you read these guides before submitting your data, and that you familiarize yourself with the PANGAEA publication style by reading about the scope of PANGAEA and by searching for and viewing datasets typical for your research field.

Please note that by registering to PANGAEA and by submitting data to PANGAEA you have agreed to our [https://www.pangaea.de/about/terms.php Terms of Use].

PANGAEA is an international data publisher, therefore we accept data submissions (including all data and metadata as well as any supplementary information) only in English. All resulting publications and our communication with data authors will also be in English.

PANGAEA datasets are intended to be self-contained and self-explanatory, i.e. a potential user of the data should be able to judge the quality and suitability for re-use (fit-for-use/fit-for-purpose). Therefore, complete metadata describing the dataset comprehensively and according to the FAIR principles must be available.

For more guidance on how to properly prepare metadata and data please see the guidelines below and our [https://www.youtube.com/@pangaeadatapublisher video tutorials]. We also offer community workshops twice a year to support our users. The winter workshop focuses on data submission issues. The workshop usually held in early summer focuses on data search and (i.a. automated) access for re-use of PANGAEA publications. If you are interested, please subscribe to our training mailing list [https://lists.pangaea.de/listinfo/training here.]

==Prepare your data and metadata for submission - a step by step guide through our submission form==
All data must be submitted using our [https://www.pangaea.de/submit/ online submission form]. Data submitted by any other means will not be processed or passed on. If you have any questions or comments about your data submission, please use either the comment field in the online submission form (step 5) or our [https://www.pangaea.de/contact/ contact form.] You can also leave a comment in the submission ticket that is automatically created when you complete the form.

===A commented guide through the submission form===
====Step 1 - Basic information====
[[File:Submission 1 Basic.png|thumb|center|]]
* Title: Provide a dataset title that briefly describes what was measured, observed, or calculated, when, where, and how. The title must be independent of the title of the manuscript/paper.
* Authors: Lists all authors of the dataset. Use full names, not initials. Authors' names are case-sensitive, do not use all capital letters for last names (example: Roe, Jane). Please provide the correct e-mail address for each author, no duplicates. If there is really no email address no-reply@pangaea.de can be entered. Fill in the affiliation field (use full names, no abbreviations, ideally according to the [https://ror.org/ Research Organization Registry] (ROR)).
* Keywords: Provide suitable keywords
* Abstract: Add a dataset abstract that is independent of the manuscript/paper abstract. The abstract should provide a concise and method-oriented description of the observation or measurement, i.e. what, when, where, why and how the data was collected. The summary should consist of meaningful running text. The format of the dataset abstract is the same as for paper abstracts. We expect more than two sentences, and ideally the length should be limited to 5000 characters. Avoid including interpretations of the data. For further information please refer to the documentation on data [[Abstract|abstracts]] for PANGAEA.
* License: Select the appropriate license for your dataset. We recommend the [https://creativecommons.org/share-your-work/cclicenses/ CC-BY 4.0] license option. Please read our [[License|wiki article]] to understand why.

====Step 2 - References====
[[File:Submission_2_References.png|thumb|center|]]
* References: Include all relevant references as full citations, not limited to a DOI including the manuscript(s) to which the data belong(s). Include any additional references mentioned in the data, methods or abstract. Include SOPs, processing or calibration reports, [https://registry.o2a-data.de/ AWI Registry] handles/links, or any other complementary documentation, if available.

====Step 3 - Projects and Grants====
[[File:Submission 3 Project.png|thumb|center|]]
* Projects: Provide names and references to related projects, grants and awards.

====Step 4 - Upload====
[[File:Submission 4 Upload.png|thumb|center|]]
* Upload: Upload your data files here. Please see below how to prepare your data files.
** More than 20 Files? → Please check the "Request upload link" box. You will receive an upload link within one to three days. Submissions containing more than 20 files may be rejected without further notice. Please replace spaces in file names before uploading.
** Files larger than 100 MB? → Please check the "Request upload link" box. Individual files must be less than 15 GB in size, but multiple files can be uploaded at the same time using the Uploader. Please replace any spaces in file names before uploading them.
* File description: This is where you describe your files. If your submission consists of more than one data table or dataset, please provide a title, authors, and abstract for each.

====Step 5 - Submit====
[[File:Submission 5 Submit.png|thumb|center]]
* Comment: Field for any request/comment for the PANGAEA editors
* Moratorium: Check, if you need a moratorium. If yes, please select the end date. The default is 6 months, if no end date is selected, the maximum is 2 years.
* Terms of Use: please read and accept our [https://www.pangaea.de/about/terms.php ToU.]

===Changes to submissions via our online form===
If you need to change or add metadata after submitting, please use the (blue) "Edit Metadata" button in the submission ticket only. The link will be sent to you automatically after you complete the form. Please note that for technical reasons direct edits in the description field of our ticket system are invalid and cannot be accepted. This is especially true for abstracts. Abstracts submitted as data files will not be considered.

== Requirements for the data files and their metadata ==
PANGAEA publishes data from earth and environmental science research in various [[Format|formats]]. Tabular data are the main focus of PANGAEA and should be prepared as TAB-delimited text-files in UTF-8 encoding, or (open) spreadsheet file formats (MS Excel .xlsx, OpenOffice & LibreOffice Calc .ods etc.). Please take a look at our [[Best practice manuals and templates|best practice manuals and templates]], which outline our requirements for relevant metadata and the structure of submitted data tables.

===Metadata about the data===
Data tables and data files are provided with metadata about the sampling/measuring stations or equipment, and the parameters/variables measured. The following list of meta-information is required for each data submission to PANGAEA.

* '''[[Campaign]]''': Were the samples or measurements relevant to your data collected during campaigns, expeditions, field trips or cruises? We subsume these under the label "Campaign", which is best described by the meta information listed below. We recommend using our template “Campaign” or the sheet "Campaign" in the excel file in our [[Best practice manuals and templates|templates]] to provide the following required information, if applicable:
** Campaign_Label, e.g. the respective cruise number
** Basis, e.g. the name of the ship, station, aircraft etc. Please leave this field blank, if no basis can be provided.
** Start date(/time) in ISO format and UTC, i.e.. YYYY-MM-DDThh:mm:ss, UTC
** End date(/time) in ISO-format and UTC, i.e. YYYY-MM-DDThh:mm:ss, UTC
** Responsible scientist(s)
** For ship expeditions start and end port
** For expeditions with German research vessels, please refer to the [https://www.pangaea.de/expeditions/ cruise inventory] and report information according to this list.

* '''[[Event]]''': An event refers to the sampling or measurement site or position for field observations, or the sampling location of organisms or media such as water used for experiments. Please refer to the [[event]] documentation for more details. Please use the text file “Event” or the sheet "Event" in the Excel workbook from our [[Best practice manuals and templates|templates]] whenever possible. Information that should be provided includes:
** Event_Label - refers to a representative short name or label for the station or locality of a sampling event. For data from expeditions with German research vessels please use the official event labels and station lists provided in the [https://www.pangaea.de/expeditions/ cruise inventory].
** Latitude and Longitude - considered mandatory event metadata both must be specified in decimal degrees and conform to WGS84 (positive for north, negative for south). For profiles, please provide start and end positions.
** [[Geocode|Elevation]] - the “[[Geocode|3rd geocode]]”. Please specify start and end elevations for profiles.
** Date/Time of sampling/measurement provided in ISO format (YYYY-MM-DDThh:mm:ss) and in UTC. An additional column with local date/time may be provided. For profiles and time series, please provide start and end date/time.
** [[Method|Device or method]] used for sampling or the measurement
** Campaign, see above
** Any other event related information, e.g. mesh size of nets, core length of sediment and ice cores, International Generic Sample Number ([https://www.igsn.org/ IGSN]).

* '''[[Parameter|Parameters]]''': In PANGAEA, the measurement variables are referred to as parameters. Entries for parameters always require the full parameter name and its unit, if available. You can see the complete list of available parameters [https://www.pangaea.de/lists/parameter/all-byname here]. Please note that parameters may also include the medium (e.g. “Temperature, air” or “Temperature, water”) or other details for disambiguation purposes. Please provide additional information on parameters, e.g. the Principal Investigator and methods as a comment within the data submission, in an additional metadata text document or in the sheet “Parameters” of our Excel [[Best practice manuals and templates|template files]]. Information to be provided:
** Parameter names of the measured or determined entities given in full, not abbreviated.
** Unit (SI units are preferred)
** Include the [[Principle investigator|Principle Investigator]] (PI) for the measured parameters. The PI is the person being responsible for the acquisition and the scientific quality of the data or a data series.
** If applicable, identify the primary instrument used to measure each specific variable/parameter, preferably in the following standardized format: "Instrument type, Manufacturer, Model name". If you did not use an instrument, please provide the methodology used instead, preferably in the following (also standardized) format: "Method type according to Reference et al. (YYYY)". Further details on how to provide instrument or method information can be found in the [[Method|respective documentation]].

===How to prepare tabular Data:===
This section summarizes the formal and structural requirements for data in tabular form. Adherence to these requirements will significantly reduce the most time-consuming aspect of our editorial work and, thus, support our efforts to reduce the overall processing time for submissions to PANGAEA significantly. Significant deviations from these requirements are therefore likely to result in rejection of the submission.

'''Structure of tabular data:'''
[[File:Data tables.png|800px|thumb|right|]]
* Submit your tables as TAB-delimited text files (UTF-8 encoding), or as (open) spreadsheet files (e.g. Libreoffice Calc .ods or MS Excel .xlsx).
* The first column should always contain the event label, followed by columns with the [[Geocode|3rd geocode]] (e.g. height/depth) and/or sample IDs and sample information. These are followed by columns containing the measured variables (parameters). Each value in a row should refer to the event and the 3rd geocode specified in columns 1 and 2.
* The first row is reserved for the column headers, which contain the full parameter names including units in square brackets.
* Multiple tables with different structures should always be provided as separate data files.
* Please use our [[Best practice manuals and templates|template files]] whenever possible to report your data in the correct way.

===How to prepare [[Binary objects|binary files]]:===
* One data file: please provide a brief description of what is contained in the file (e.g. in the ‘File description’ field in Step 4 - “Upload” of our submission form).
* More than one data file: please include a summary table, provided as TAB-delimited text file (UTF-8 encoding) or spreadsheet including file names, a brief description of each file (< 255 characters including spaces) and corresponding [[Geocode|Geocodes]].
* Use filenames without spaces
* Request an upload link if you are submitting more than 20 files or files larger than 100 Mb (see Step 4 - “Upload” of our submission form). Individual files must be less than 15 GB in size.

==Additional information and useful links==

Frequently asked questions about data submission are listed here [[FAQ]].

Do you have questions about the status of your submission or the status of your submission? Please contact us via your submission ticket or via our [https://www.pangaea.de/contact/ contact form].

Binary objects

2025-03-18T09:58:07Z

Awittmann: Added maximum file size of 15 GB

Binary files with specific formats (e.g. shape files, netCDF, segy, images, videos, ...) will be archived as links to files. For these data types submissions (even if <20 files or <100 MB), please always request an upload link during the submission - see screenshot. Individual files must be less than 15 GB in size.
[[File:Request upload link.png|alt=Screenshot from submission form: request upload link|thumb|Screenshot from submission form: request upload link]]

In addition to the data files, please prepare a '''file list''' including:
* [[Event]]
* Latitude, Longitude (coordinated universal time, UTC)
* Date/Time (ISO-format, e.g. 1954-04-07T13:34:11)
* File names including their extension. The names should not contain spaces and special symbols.

Further columns with metadata are needed/welcome (depending on the context), for example:
* Data description / File content
* Third [[geocode]], such as Elevation, Depth, etc.
* Relative X and Y coordinates, if for example only the start and the end of the survey have known absolute georeference
* Comment

Further (automatic) columns can be configured in the table by the PANGAEA editors (these do not have to be added by the authors), including:
* File size
* Character set
* Media type
* MD5 hash

=== File list templates ===

[[Media:Template binary JPG.tab|'''photos in JPG format''' (tab-separated text file)]]
[[Media:Template binary nc.tab|'''netCDF files''' (tab-separated text file)]]
[[Media:Template binary CTD raw.tab|'''raw CTD files''' (tab-separated text file)]]

== Metadata – [[Event|Events]] table ==

The Event table is not needed, when the [[Event|Events]] are already present in PANGAEA, see https://www.pangaea.de/expeditions/ for checking. For further info see [[Station lists]]. If the event information '''cannot''' be found under https://www.pangaea.de/expeditions, please provide us with a table of additional metadata, using the template below. This will give an overview of the when, where and how the data were collected:

* Event label, unique identifier of sampling time and location.
* Campaign, e.g. ship cruise ID, please read: [[Campaign]].
* Device or method used to collect a sample or (experimental) organism, please read: [[Method]].
* Date and time in ISO-format (e.g. 1954-04-07T13:34:11) as coordinated universal time (UTC), start and end date/time must be provided in separate columns.
* Latitude and longitude in decimal degrees (S and W are negative) of data collection. For transects, start and end latitude and longitude should be provided in separate columns.
* Elevation (altitude, sea bottom depth, negative below sea level) is optional. For transects, start and end elevation must be provided in separate columns.

=== Event template with further instructions===
[[Media:Event template.xlsx|'''Event template''' (xlsx file)]]

== Naming of files ==
Please '''avoid''' the following when naming your files:

* NUL, , /, :, *, ?, ", <, >, |
* special characters such as ä, ö, ü
* spaces within file names
* . or .. and control characters

== Examples of published datasets with binary objects ==
* Photos, underwater: [https://doi.pangaea.de/10.1594/PANGAEA.936188?format=html#download Purser, A et al. (2021): Seabed photographs taken along OFOS profile PS124_8-1 during POLARSTERN cruise PS124. PANGAEA, https://doi.org/10.1594/PANGAEA.936188]
* Photos, underwater, with relative coodrinates: [https://doi.pangaea.de/10.1594/PANGAEA.958362?format=html#download Anhaus, P et al. (2023): Upward-looking still images from ROV survey PS122/1_6-16 on 2019-11-05, survey 1. PANGAEA, https://doi.org/10.1594/PANGAEA.958362]
* Photos, terrestrial: [https://doi.pangaea.de/10.1594/PANGAEA.955824?format=html#download Gómez Izquierdo, D R & Quartino, M L (2023): Photographs of Potter Cove, King George Island, looking northeast towards glacier in 2023. Instituto Antártico Argentino, Buenos Aires, Argentina, PANGAEA, https://doi.org/10.1594/PANGAEA.955824]
* Tabular data with additional photos: [https://doi.pangaea.de/10.1594/PANGAEA.927181?format=html#download Sander, Let al. (2021): Properties of a subfossil oyster bed, Grab 5. PANGAEA, https://doi.org/10.1594/PANGAEA.927181]
* NetCDF files: [https://doi.pangaea.de/10.1594/PANGAEA.944101?format=html#download Mech, M et al. (2022): Microwave brightness temperature measurements during the MOSAiC-ACA Arctic airborne campaign in late summer 2020 out of Svalbard. PANGAEA, https://doi.org/10.1594/PANGAEA.944101]
* Oceanography (CTD) raw data: [https://doi.pangaea.de/10.1594/PANGAEA.957843?format=html#download Tippenhauer, S et al. (2022): Raw data of physical oceanography during RV POLARSTERN cruises PS130/1 and PS130/2. PANGAEA, https://doi.org/10.1594/PANGAEA.957843]
* Bathymetry processed data: [https://doi.pangaea.de/10.1594/PANGAEA.956742?format=html#download Steffen, Melanie et al. (2023): Multibeam bathymetry processed data (Kongsberg EM 122 transit dataset) of RV MARIA S. MERIAN during cruise MSM79/2, Atlantic Ocean. PANGAEA, https://doi.org/10.1594/PANGAEA.956742]

Vertical sediment profile

2025-01-21T09:58:04Z

Awittmann: /* Metadata Parameter */

{{Construction}}

Please read and follow our [[Authors Guides|Authors Guides]] when preparing your [https://www.pangaea.de/submit/ data submission].
We recommend to use the topic specific templates and to follow the instructions here. The following defines frequent data types and summarizes how to prepare geological, paleontological, geochemical and mineralogical data collected in the field for submission to PANGAEA.

== Coring/Drilling==
This data type describes measurements in sediment and rock cores. These two data publications can serve as an example:

''Hättig, Katrin; Varma, Devika; van der Meer, Marcel T J; Schouten, Stefan (2023): Hydrogen isotopic composition of alkenones and oxygen isotopes of benthic foraminifera from ODP Site 202-1235. PANGAEA, https://doi.org/10.1594/PANGAEA.958880''

''Biskaborn, Boris K; Pfalz, Gregor; Wieczorek, Mareike; Heim, Birgit; Meyer, Hanno; Pestryakova, Luidmila A; Herzschuh, Ulrike; Diekmann, Bernhard (2023): Standardized diatom data of sediment core PG2201 from Lake Malaya Chabyda (Yakutia, Russia). PANGAEA, https://doi.org/10.1594/PANGAEA.956860''

This [[Media:PANGAEA Template Sed Core.xlsx|'''Template for sediment/rock cores''']] might help you for your [[Authors Guides|Data submission]]. Drillings are described with a number of metadata. These are listed below and each corresponds to a data sheet in the template.

=== Metadata Campaign ===
Please fill the [[Campaign]] sheet with:
* Cruise/expedition label
* Start and end date (in ISO 8601)
* Basis = ship or research platform
* Chief Scientist

=== Metadata Event ===
Please fill the [[Event]] sheet with:
* Event label, name of the core. You can also specify an optional event label
* Device/Method with which the sediment core was taken
* Latitude, longitude, in decimal degree
* Elevation, negative if below sea level
* Date/Time of sampling (in ISO 8601)
* Campaign of sampling
* [https://registry.awi.de registry.awi] link (formaly known as sensor.awi)
* International Generic Sample Number [https://www.igsn.org ISGN] link/handle
* Information about penetration and/or recovery
* Location of drilling/coring

=== Metadata Parameter ===
Please fill the [[Parameter]] sheet with:
* Give all parameters as full names, no abbreviations
* Full name applies especially to species names. If possible, check the species names via [https://www.marinespecies.org/aphia.php?p=search WoRMS] or another taxonomic database.
* Unit, SI units are preferred
* Principle Investigator ([[Principle investigator|PI]]) for the parameters. The Principle investigator (PI) is the person being responsible for the scientific quality of a data series
* [[Method|method]] of measurement for each parameter

=== Data ===
Please see the Data sheet and use it as a guide to structure your data table:
* First column: Event label
* First line: full parameter names including the unit, given in square brackets
* Give the depth below seafloor (or mcd, rmcd) or the depth below earth surface in meter = DEPTH, sediment/rock, see [[Geocode]] description.
* For depth intervals please specify three columns with average depth, minimum and maximum depth
* In addition geological data benefit from an age scale. Please give the age in [ka] as additional column, if available
* In addition, provide sample labels and IGSN, if available

== Outcrop/Geological Sections ==
This data type describes measurements in sediment and rock sampled in outcrops and geological profils and sections. This data publication can serve as an example:

''Martínez-Braceras, Naroa; Franceschetti, Gloria; Payros, Aitor; Monechi, Simonetta; Dinarès-Turell, Jaume (2022): Calcareous nannofossil from the hemipelagic lower Ypresian Arnakatxa section (Basque-Cantabrian basin, western Pyrenees). PANGAEA, https://doi.org/10.1594/PANGAEA.943590''

This '''[[Media:PANGAEA Template Outcrop.xlsx|Template for Outcrop/Geological Section]]'''
''' might help you for your [[Authors Guides|Data submission]]. Outcrops and profiles are described with a number of metadata. These are listed below and each corresponds to a data sheet in the template.

=== Metadate Campaign ===
Please fill up the [[Campaign]] sheet with:
* Expedition label
* Start and End date (in ISO 8601)
* Basis = Research platform, if available
* Chief Scientist

=== Metadata Event ===
Please fill up the [[Event]] sheet with:
* Event label, name of the outcrop/section. You can also specify an optional event label
* Latitude, Longitude, in decimal degree. If start and end are very different in position, please specify both latitudes/longitudes
* Elevation
* Date/Time of sampling (in ISO 8601)
* Campaign of sampling
* [https://registry.awi.de registry.awi] link (formaly know as sensor.awi)
* International Generic Sample Number [https://www.igsn.org ISGN] link/handle
* Location of outcrop/section

=== Metadata Parameter ===
Please fill up the [[Parameter]] sheet with:
* Give all parameters as full names, no abbreviations
* Full name applies especially to species names. If possible, check the species names via [https://www.marinespecies.org/aphia.php?p=search WoRMS] or another taxonomic database.
* Unit, SI units are preferred
* Principle Investigator ([[Principle investigator|PI]]) for the parameters. The Principle investigator (PI) is the person being responsible for the scientific quality of a data series
* [[Method|method]] of measurement for each parameter

=== Data ===
Please see the Data sheet and use it as a guide to structure your data table:
* First column: Event label
* First line: full parameter names including the unit, given in square brackets
* Give the SECTION Hight in [m]. This is the hight from outcrop/section base or from a specific defined marker horizon, see [[Geocode]] description.
* For SECTION height intervals please specify three columns with average height, minimum and maximum height
* In addition geological data benefit from an age scale. Please give the age in [ka] as additional column, if available
* In addition, provide sample labels and IGSN, if available

== Surface Sediment Samples/Time Slices ==
This data type describes measurements of surface sediment samples. These samples can be taken by divers gears such as MUC, GKG or Grabs. The data type can also be applied to time slices in different sediment cores. Multiple short cores can also be represented in this data type. These two data publications can serve as an example:

''Przibilla, Anna; Sanders, Tina; Neumann, Andreas; Nantke, Carla (2023): Pore water nutrient concentrations from sediments sampled during RV Alkor cruise AL557. PANGAEA, https://doi.org/10.1594/PANGAEA.956878''

''de Haas, Henk (2022): Dry bulk density, organic carbon and organic nitrogen in surface sediments of the North Sea sampled in 1994/1995. PANGAEA, https://doi.org/10.1594/PANGAEA.942428''

This '''[[Media:PANGAEA Template surface.xlsx| Template for Surface Sediment Samples]]''' might help you for your [[Authors Guides|Data submission]]. The template is designed for sediment surface samples and also for comparison of time slices in diverse sediment cores. This type of datasets needs a number of metadata. These are listed below and each corresponds to a data sheet in the template.

=== Metadate Campaign ===
Please fill up the [[Campaign]] sheet with:
* Cruise/expedition label, please list all cruises/expeditions of your study
* Start and End date (in ISO 8601)
* Basis = ship or research platform
* Chief Scientist

=== Metadata Event ===
Please fill up the [[Event]] sheet with:
* Event label, name of the core or grab. You can also specify an optional event label
* Device/Method with which the sediment core was taken
* Latitude, Longitude, in decimal degree
* Elevation
* Date/Time of sampling (in ISO 8601)
* Campaign of sampling
* [https://registry.awi.de registry.awi] link (formaly know as sensor.awi)
* International Generic Sample Number [https://www.igsn.org ISGN] link/handle
* Location of drilling/coring

=== Metadata Parameter ===
Please fill up the [[Parameter]] sheet with:
* Give all parameters as full names, no abbreviations
* Full name applies especially to species names. If possible, check the species names via [https://www.marinespecies.org/aphia.php?p=search WoRMS] or another taxonomic database.
* Unit, SI units are preferred
* Principle Investigator ([[Principle investigator|PI]]) for the parameters. The Principle investigator (PI) is the person being responsible for the scientific quality of a data series
* [[Method|method]] of measurement for each parameter

=== Data ===
Please see the Data sheet and use it as a guide to structure your data table:
* First column: Event label
* First line: full parameter names including the unit, given in square brackets
* Give columns with latitude, longitude and elevation for each sample
* Give the depth below seafloor (or mcd, rmcd) or the depth below earth surface in meter = DEPTH, sediment/rock, see [[Geocode]] description. For surface sediments please use the value “0”.
* For depth intervals please specify three columns with average depth, minimum and maximum depth
* In addition geological data benefit from an age scale. Please give the age in [ka] as additional column, if you do not have Recent samples, but geological time slices
* In addition, provide sample labels and IGSN, if available

== Rock Samples/Mineralogy/Petrology ==
Geochemistry and age determinations on rocks or individual minerals are described with this data type. This data publication can serve as an example:

''Breitfeld, H Tim (2023): Detrital zircon U-Pb geochronology of (Plio-)Pleistocene sediments in West Sarawak. PANGAEA, https://doi.org/10.1594/PANGAEA.959520''

This '''[[Media:PANGAEA Template Rock Min.xlsx| Template for Rock Samples/Mineralogy/Petrology]]''' might help you for your [[Authors Guides|Data submission]]. The template is designed for rock samples that focus on the chemical composition and age determinations of minerals and rocks. This type of datasets needs a number of metadata. These are listed below and each corresponds to a data sheet in the template.

=== Metadate Campaign ===
Please fill up the [[Campaign]] sheet with:
* Cruise/expedition label
* Start and End date (in ISO 8601)
* Basis = ship or research platform
* Chief Scientist

=== Metadata Event ===
Please fill up the [[Event]] sheet with:
* Event label, name of sampling site. You can also specify an optional event label
* Device/Method with which the sample was taken
* Latitude, Longitude, in decimal degree
* Elevation
* Date/Time of sampling (in ISO 8601)
* Campaign of sampling
* [https://registry.awi.de registry.awi] link (formaly know as sensor.awi)
* International Generic Sample Number [https://www.igsn.org ISGN] link/handle
* Location of sampling

=== Metadata Parameter ===
Please fill up the [[Parameter]] sheet with:
* Give all parameters as full names, no abbreviations
* Please give the full parameter names, chemical elements may be abbreviated
* Unit, SI units are preferred
* Principle Investigator ([[Principle investigator|PI]]) for the parameters. The Principle investigator (PI) is the person being responsible for the scientific quality of a data series
* [[Method|method]] of measurement for each parameter

=== Data ===
Please see the Data sheet and use it as a guide to structure your data table:
* First column: Event label
* First line: full parameter names including the unit, given in square brackets
* If you have two-dimensional samples, give columns with latitude, longitude and elevation for each sample
* If you have samples from drilling, give the depth below seafloor (or mcd, rmcd) or the depth below earth surface in meter = DEPTH, sediment/rock, see [[Geocode]] description.
* If you have samples from an outcrop/section, give the SECTION Hight in [m]. This is the hight from outcrop/section base or from a specific defined marker horizon, see [[Geocode]] description.
* In addition geological data benefit from an age scale. Please give the age of the sample (not mineral) in [ka] as additional column. You may give additional the age in Ma.
* In addition, provide sample labels and IGSN, if available

Vertical sediment profile

2025-01-21T09:57:43Z

Awittmann: /* Coring/Drilling */ corrected typos

{{Construction}}

Please read and follow our [[Authors Guides|Authors Guides]] when preparing your [https://www.pangaea.de/submit/ data submission].
We recommend to use the topic specific templates and to follow the instructions here. The following defines frequent data types and summarizes how to prepare geological, paleontological, geochemical and mineralogical data collected in the field for submission to PANGAEA.

== Coring/Drilling==
This data type describes measurements in sediment and rock cores. These two data publications can serve as an example:

''Hättig, Katrin; Varma, Devika; van der Meer, Marcel T J; Schouten, Stefan (2023): Hydrogen isotopic composition of alkenones and oxygen isotopes of benthic foraminifera from ODP Site 202-1235. PANGAEA, https://doi.org/10.1594/PANGAEA.958880''

''Biskaborn, Boris K; Pfalz, Gregor; Wieczorek, Mareike; Heim, Birgit; Meyer, Hanno; Pestryakova, Luidmila A; Herzschuh, Ulrike; Diekmann, Bernhard (2023): Standardized diatom data of sediment core PG2201 from Lake Malaya Chabyda (Yakutia, Russia). PANGAEA, https://doi.org/10.1594/PANGAEA.956860''

This [[Media:PANGAEA Template Sed Core.xlsx|'''Template for sediment/rock cores''']] might help you for your [[Authors Guides|Data submission]]. Drillings are described with a number of metadata. These are listed below and each corresponds to a data sheet in the template.

=== Metadata Campaign ===
Please fill the [[Campaign]] sheet with:
* Cruise/expedition label
* Start and end date (in ISO 8601)
* Basis = ship or research platform
* Chief Scientist

=== Metadata Event ===
Please fill the [[Event]] sheet with:
* Event label, name of the core. You can also specify an optional event label
* Device/Method with which the sediment core was taken
* Latitude, longitude, in decimal degree
* Elevation, negative if below sea level
* Date/Time of sampling (in ISO 8601)
* Campaign of sampling
* [https://registry.awi.de registry.awi] link (formaly known as sensor.awi)
* International Generic Sample Number [https://www.igsn.org ISGN] link/handle
* Information about penetration and/or recovery
* Location of drilling/coring

=== Metadata Parameter ===
Please fill up the [[Parameter]] sheet with:
* Give all parameters as full names, no abbreviations
* Full name applies especially to species names. If possible, check the species names via [https://www.marinespecies.org/aphia.php?p=search WoRMS] or another taxonomic database.
* Unit, SI units are preferred
* Principle Investigator ([[Principle investigator|PI]]) for the parameters. The Principle investigator (PI) is the person being responsible for the scientific quality of a data series
* [[Method|method]] of measurement for each parameter

=== Data ===
Please see the Data sheet and use it as a guide to structure your data table:
* First column: Event label
* First line: full parameter names including the unit, given in square brackets
* Give the depth below seafloor (or mcd, rmcd) or the depth below earth surface in meter = DEPTH, sediment/rock, see [[Geocode]] description.
* For depth intervals please specify three columns with average depth, minimum and maximum depth
* In addition geological data benefit from an age scale. Please give the age in [ka] as additional column, if available
* In addition, provide sample labels and IGSN, if available

== Outcrop/Geological Sections ==
This data type describes measurements in sediment and rock sampled in outcrops and geological profils and sections. This data publication can serve as an example:

''Martínez-Braceras, Naroa; Franceschetti, Gloria; Payros, Aitor; Monechi, Simonetta; Dinarès-Turell, Jaume (2022): Calcareous nannofossil from the hemipelagic lower Ypresian Arnakatxa section (Basque-Cantabrian basin, western Pyrenees). PANGAEA, https://doi.org/10.1594/PANGAEA.943590''

This '''[[Media:PANGAEA Template Outcrop.xlsx|Template for Outcrop/Geological Section]]'''
''' might help you for your [[Authors Guides|Data submission]]. Outcrops and profiles are described with a number of metadata. These are listed below and each corresponds to a data sheet in the template.

=== Metadate Campaign ===
Please fill up the [[Campaign]] sheet with:
* Expedition label
* Start and End date (in ISO 8601)
* Basis = Research platform, if available
* Chief Scientist

=== Metadata Event ===
Please fill up the [[Event]] sheet with:
* Event label, name of the outcrop/section. You can also specify an optional event label
* Latitude, Longitude, in decimal degree. If start and end are very different in position, please specify both latitudes/longitudes
* Elevation
* Date/Time of sampling (in ISO 8601)
* Campaign of sampling
* [https://registry.awi.de registry.awi] link (formaly know as sensor.awi)
* International Generic Sample Number [https://www.igsn.org ISGN] link/handle
* Location of outcrop/section

=== Metadata Parameter ===
Please fill up the [[Parameter]] sheet with:
* Give all parameters as full names, no abbreviations
* Full name applies especially to species names. If possible, check the species names via [https://www.marinespecies.org/aphia.php?p=search WoRMS] or another taxonomic database.
* Unit, SI units are preferred
* Principle Investigator ([[Principle investigator|PI]]) for the parameters. The Principle investigator (PI) is the person being responsible for the scientific quality of a data series
* [[Method|method]] of measurement for each parameter

=== Data ===
Please see the Data sheet and use it as a guide to structure your data table:
* First column: Event label
* First line: full parameter names including the unit, given in square brackets
* Give the SECTION Hight in [m]. This is the hight from outcrop/section base or from a specific defined marker horizon, see [[Geocode]] description.
* For SECTION height intervals please specify three columns with average height, minimum and maximum height
* In addition geological data benefit from an age scale. Please give the age in [ka] as additional column, if available
* In addition, provide sample labels and IGSN, if available

== Surface Sediment Samples/Time Slices ==
This data type describes measurements of surface sediment samples. These samples can be taken by divers gears such as MUC, GKG or Grabs. The data type can also be applied to time slices in different sediment cores. Multiple short cores can also be represented in this data type. These two data publications can serve as an example:

''Przibilla, Anna; Sanders, Tina; Neumann, Andreas; Nantke, Carla (2023): Pore water nutrient concentrations from sediments sampled during RV Alkor cruise AL557. PANGAEA, https://doi.org/10.1594/PANGAEA.956878''

''de Haas, Henk (2022): Dry bulk density, organic carbon and organic nitrogen in surface sediments of the North Sea sampled in 1994/1995. PANGAEA, https://doi.org/10.1594/PANGAEA.942428''

This '''[[Media:PANGAEA Template surface.xlsx| Template for Surface Sediment Samples]]''' might help you for your [[Authors Guides|Data submission]]. The template is designed for sediment surface samples and also for comparison of time slices in diverse sediment cores. This type of datasets needs a number of metadata. These are listed below and each corresponds to a data sheet in the template.

=== Metadate Campaign ===
Please fill up the [[Campaign]] sheet with:
* Cruise/expedition label, please list all cruises/expeditions of your study
* Start and End date (in ISO 8601)
* Basis = ship or research platform
* Chief Scientist

=== Metadata Event ===
Please fill up the [[Event]] sheet with:
* Event label, name of the core or grab. You can also specify an optional event label
* Device/Method with which the sediment core was taken
* Latitude, Longitude, in decimal degree
* Elevation
* Date/Time of sampling (in ISO 8601)
* Campaign of sampling
* [https://registry.awi.de registry.awi] link (formaly know as sensor.awi)
* International Generic Sample Number [https://www.igsn.org ISGN] link/handle
* Location of drilling/coring

=== Metadata Parameter ===
Please fill up the [[Parameter]] sheet with:
* Give all parameters as full names, no abbreviations
* Full name applies especially to species names. If possible, check the species names via [https://www.marinespecies.org/aphia.php?p=search WoRMS] or another taxonomic database.
* Unit, SI units are preferred
* Principle Investigator ([[Principle investigator|PI]]) for the parameters. The Principle investigator (PI) is the person being responsible for the scientific quality of a data series
* [[Method|method]] of measurement for each parameter

=== Data ===
Please see the Data sheet and use it as a guide to structure your data table:
* First column: Event label
* First line: full parameter names including the unit, given in square brackets
* Give columns with latitude, longitude and elevation for each sample
* Give the depth below seafloor (or mcd, rmcd) or the depth below earth surface in meter = DEPTH, sediment/rock, see [[Geocode]] description. For surface sediments please use the value “0”.
* For depth intervals please specify three columns with average depth, minimum and maximum depth
* In addition geological data benefit from an age scale. Please give the age in [ka] as additional column, if you do not have Recent samples, but geological time slices
* In addition, provide sample labels and IGSN, if available

== Rock Samples/Mineralogy/Petrology ==
Geochemistry and age determinations on rocks or individual minerals are described with this data type. This data publication can serve as an example:

''Breitfeld, H Tim (2023): Detrital zircon U-Pb geochronology of (Plio-)Pleistocene sediments in West Sarawak. PANGAEA, https://doi.org/10.1594/PANGAEA.959520''

This '''[[Media:PANGAEA Template Rock Min.xlsx| Template for Rock Samples/Mineralogy/Petrology]]''' might help you for your [[Authors Guides|Data submission]]. The template is designed for rock samples that focus on the chemical composition and age determinations of minerals and rocks. This type of datasets needs a number of metadata. These are listed below and each corresponds to a data sheet in the template.

=== Metadate Campaign ===
Please fill up the [[Campaign]] sheet with:
* Cruise/expedition label
* Start and End date (in ISO 8601)
* Basis = ship or research platform
* Chief Scientist

=== Metadata Event ===
Please fill up the [[Event]] sheet with:
* Event label, name of sampling site. You can also specify an optional event label
* Device/Method with which the sample was taken
* Latitude, Longitude, in decimal degree
* Elevation
* Date/Time of sampling (in ISO 8601)
* Campaign of sampling
* [https://registry.awi.de registry.awi] link (formaly know as sensor.awi)
* International Generic Sample Number [https://www.igsn.org ISGN] link/handle
* Location of sampling

=== Metadata Parameter ===
Please fill up the [[Parameter]] sheet with:
* Give all parameters as full names, no abbreviations
* Please give the full parameter names, chemical elements may be abbreviated
* Unit, SI units are preferred
* Principle Investigator ([[Principle investigator|PI]]) for the parameters. The Principle investigator (PI) is the person being responsible for the scientific quality of a data series
* [[Method|method]] of measurement for each parameter

=== Data ===
Please see the Data sheet and use it as a guide to structure your data table:
* First column: Event label
* First line: full parameter names including the unit, given in square brackets
* If you have two-dimensional samples, give columns with latitude, longitude and elevation for each sample
* If you have samples from drilling, give the depth below seafloor (or mcd, rmcd) or the depth below earth surface in meter = DEPTH, sediment/rock, see [[Geocode]] description.
* If you have samples from an outcrop/section, give the SECTION Hight in [m]. This is the hight from outcrop/section base or from a specific defined marker horizon, see [[Geocode]] description.
* In addition geological data benefit from an age scale. Please give the age of the sample (not mineral) in [ka] as additional column. You may give additional the age in Ma.
* In addition, provide sample labels and IGSN, if available

Vertical sediment profile

2025-01-21T09:44:02Z

Awittmann: /* Metadate Campaign */ Corrected typo

{{Construction}}

Please read and follow our [[Authors Guides|Authors Guides]] when preparing your [https://www.pangaea.de/submit/ data submission].
We recommend to use the topic specific templates and to follow the instructions here. The following defines frequent data types and summarizes how to prepare geological, paleontological, geochemical and mineralogical data collected in the field for submission to PANGAEA.

== Coring/Drilling==
This data type describes measurements in sediment and rock cores. These two data publications can serve as an example:

''Hättig, Katrin; Varma, Devika; van der Meer, Marcel T J; Schouten, Stefan (2023): Hydrogen isotopic composition of alkenones and oxygen isotopes of benthic foraminifera from ODP Site 202-1235. PANGAEA, https://doi.org/10.1594/PANGAEA.958880''

''Biskaborn, Boris K; Pfalz, Gregor; Wieczorek, Mareike; Heim, Birgit; Meyer, Hanno; Pestryakova, Luidmila A; Herzschuh, Ulrike; Diekmann, Bernhard (2023): Standardized diatom data of sediment core PG2201 from Lake Malaya Chabyda (Yakutia, Russia). PANGAEA, https://doi.org/10.1594/PANGAEA.956860''

This [[Media:PANGAEA Template Sed Core.xlsx|'''Template for sediment/rock cores''']] might help you for your [[Authors Guides|Data submission]]. Drillings are described with a number of metadata. These are listed below and each corresponds to a data sheet in the template.

=== Metadata Campaign ===
Please fill up the [[Campaign]] sheet with:
* Cruise/expedition label
* Start and End date (in ISO 8601)
* Basis = ship or research platform
* Chief Scientist

=== Metadata Event ===
Please fill up the [[Event]] sheet with:
* Event label, name of the core. You can also specify an optional event label
* Device/Method with which the sediment core was taken
* Latitude, Longitude, in decimal degree
* Elevation, negativ if below sea level
* Date/Time of sampling (in ISO 8601 )
* Campaign of sampling
* [https://registry.awi.de registry.awi] link (formaly know as sensor.awi)
* International Generic Sample Number [https://www.igsn.org ISGN] link/handle
* Information about penetration and/or recovery
* Location of drilling/coring

=== Metadata Parameter ===
Please fill up the [[Parameter]] sheet with:
* Give all parameters as full names, no abbreviations
* Full name applies especially to species names. If possible, check the species names via [https://www.marinespecies.org/aphia.php?p=search WoRMS] or another taxonomic database.
* Unit, SI units are preferred
* Principle Investigator ([[Principle investigator|PI]]) for the parameters. The Principle investigator (PI) is the person being responsible for the scientific quality of a data series
* [[Method|method]] of measurement for each parameter

=== Data ===
Please see the Data sheet and use it as a guide to structure your data table:
* First column: Event label
* First line: full parameter names including the unit, given in square brackets
* Give the depth below seafloor (or mcd, rmcd) or the depth below earth surface in meter = DEPTH, sediment/rock, see [[Geocode]] description.
* For depth intervals please specify three columns with average depth, minimum and maximum depth
* In addition geological data benefit from an age scale. Please give the age in [ka] as additional column, if available
* In addition, provide sample labels and IGSN, if available

== Outcrop/Geological Sections ==
This data type describes measurements in sediment and rock sampled in outcrops and geological profils and sections. This data publication can serve as an example:

''Martínez-Braceras, Naroa; Franceschetti, Gloria; Payros, Aitor; Monechi, Simonetta; Dinarès-Turell, Jaume (2022): Calcareous nannofossil from the hemipelagic lower Ypresian Arnakatxa section (Basque-Cantabrian basin, western Pyrenees). PANGAEA, https://doi.org/10.1594/PANGAEA.943590''

This '''[[Media:PANGAEA Template Outcrop.xlsx|Template for Outcrop/Geological Section]]'''
''' might help you for your [[Authors Guides|Data submission]]. Outcrops and profiles are described with a number of metadata. These are listed below and each corresponds to a data sheet in the template.

=== Metadate Campaign ===
Please fill up the [[Campaign]] sheet with:
* Expedition label
* Start and End date (in ISO 8601)
* Basis = Research platform, if available
* Chief Scientist

=== Metadata Event ===
Please fill up the [[Event]] sheet with:
* Event label, name of the outcrop/section. You can also specify an optional event label
* Latitude, Longitude, in decimal degree. If start and end are very different in position, please specify both latitudes/longitudes
* Elevation
* Date/Time of sampling (in ISO 8601)
* Campaign of sampling
* [https://registry.awi.de registry.awi] link (formaly know as sensor.awi)
* International Generic Sample Number [https://www.igsn.org ISGN] link/handle
* Location of outcrop/section

=== Metadata Parameter ===
Please fill up the [[Parameter]] sheet with:
* Give all parameters as full names, no abbreviations
* Full name applies especially to species names. If possible, check the species names via [https://www.marinespecies.org/aphia.php?p=search WoRMS] or another taxonomic database.
* Unit, SI units are preferred
* Principle Investigator ([[Principle investigator|PI]]) for the parameters. The Principle investigator (PI) is the person being responsible for the scientific quality of a data series
* [[Method|method]] of measurement for each parameter

=== Data ===
Please see the Data sheet and use it as a guide to structure your data table:
* First column: Event label
* First line: full parameter names including the unit, given in square brackets
* Give the SECTION Hight in [m]. This is the hight from outcrop/section base or from a specific defined marker horizon, see [[Geocode]] description.
* For SECTION height intervals please specify three columns with average height, minimum and maximum height
* In addition geological data benefit from an age scale. Please give the age in [ka] as additional column, if available
* In addition, provide sample labels and IGSN, if available

== Surface Sediment Samples/Time Slices ==
This data type describes measurements of surface sediment samples. These samples can be taken by divers gears such as MUC, GKG or Grabs. The data type can also be applied to time slices in different sediment cores. Multiple short cores can also be represented in this data type. These two data publications can serve as an example:

''Przibilla, Anna; Sanders, Tina; Neumann, Andreas; Nantke, Carla (2023): Pore water nutrient concentrations from sediments sampled during RV Alkor cruise AL557. PANGAEA, https://doi.org/10.1594/PANGAEA.956878''

''de Haas, Henk (2022): Dry bulk density, organic carbon and organic nitrogen in surface sediments of the North Sea sampled in 1994/1995. PANGAEA, https://doi.org/10.1594/PANGAEA.942428''

This '''[[Media:PANGAEA Template surface.xlsx| Template for Surface Sediment Samples]]''' might help you for your [[Authors Guides|Data submission]]. The template is designed for sediment surface samples and also for comparison of time slices in diverse sediment cores. This type of datasets needs a number of metadata. These are listed below and each corresponds to a data sheet in the template.

=== Metadate Campaign ===
Please fill up the [[Campaign]] sheet with:
* Cruise/expedition label, please list all cruises/expeditions of your study
* Start and End date (in ISO 8601)
* Basis = ship or research platform
* Chief Scientist

=== Metadata Event ===
Please fill up the [[Event]] sheet with:
* Event label, name of the core or grab. You can also specify an optional event label
* Device/Method with which the sediment core was taken
* Latitude, Longitude, in decimal degree
* Elevation
* Date/Time of sampling (in ISO 8601)
* Campaign of sampling
* [https://registry.awi.de registry.awi] link (formaly know as sensor.awi)
* International Generic Sample Number [https://www.igsn.org ISGN] link/handle
* Location of drilling/coring

=== Metadata Parameter ===
Please fill up the [[Parameter]] sheet with:
* Give all parameters as full names, no abbreviations
* Full name applies especially to species names. If possible, check the species names via [https://www.marinespecies.org/aphia.php?p=search WoRMS] or another taxonomic database.
* Unit, SI units are preferred
* Principle Investigator ([[Principle investigator|PI]]) for the parameters. The Principle investigator (PI) is the person being responsible for the scientific quality of a data series
* [[Method|method]] of measurement for each parameter

=== Data ===
Please see the Data sheet and use it as a guide to structure your data table:
* First column: Event label
* First line: full parameter names including the unit, given in square brackets
* Give columns with latitude, longitude and elevation for each sample
* Give the depth below seafloor (or mcd, rmcd) or the depth below earth surface in meter = DEPTH, sediment/rock, see [[Geocode]] description. For surface sediments please use the value “0”.
* For depth intervals please specify three columns with average depth, minimum and maximum depth
* In addition geological data benefit from an age scale. Please give the age in [ka] as additional column, if you do not have Recent samples, but geological time slices
* In addition, provide sample labels and IGSN, if available

== Rock Samples/Mineralogy/Petrology ==
Geochemistry and age determinations on rocks or individual minerals are described with this data type. This data publication can serve as an example:

''Breitfeld, H Tim (2023): Detrital zircon U-Pb geochronology of (Plio-)Pleistocene sediments in West Sarawak. PANGAEA, https://doi.org/10.1594/PANGAEA.959520''

This '''[[Media:PANGAEA Template Rock Min.xlsx| Template for Rock Samples/Mineralogy/Petrology]]''' might help you for your [[Authors Guides|Data submission]]. The template is designed for rock samples that focus on the chemical composition and age determinations of minerals and rocks. This type of datasets needs a number of metadata. These are listed below and each corresponds to a data sheet in the template.

=== Metadate Campaign ===
Please fill up the [[Campaign]] sheet with:
* Cruise/expedition label
* Start and End date (in ISO 8601)
* Basis = ship or research platform
* Chief Scientist

=== Metadata Event ===
Please fill up the [[Event]] sheet with:
* Event label, name of sampling site. You can also specify an optional event label
* Device/Method with which the sample was taken
* Latitude, Longitude, in decimal degree
* Elevation
* Date/Time of sampling (in ISO 8601)
* Campaign of sampling
* [https://registry.awi.de registry.awi] link (formaly know as sensor.awi)
* International Generic Sample Number [https://www.igsn.org ISGN] link/handle
* Location of sampling

=== Metadata Parameter ===
Please fill up the [[Parameter]] sheet with:
* Give all parameters as full names, no abbreviations
* Please give the full parameter names, chemical elements may be abbreviated
* Unit, SI units are preferred
* Principle Investigator ([[Principle investigator|PI]]) for the parameters. The Principle investigator (PI) is the person being responsible for the scientific quality of a data series
* [[Method|method]] of measurement for each parameter

=== Data ===
Please see the Data sheet and use it as a guide to structure your data table:
* First column: Event label
* First line: full parameter names including the unit, given in square brackets
* If you have two-dimensional samples, give columns with latitude, longitude and elevation for each sample
* If you have samples from drilling, give the depth below seafloor (or mcd, rmcd) or the depth below earth surface in meter = DEPTH, sediment/rock, see [[Geocode]] description.
* If you have samples from an outcrop/section, give the SECTION Hight in [m]. This is the hight from outcrop/section base or from a specific defined marker horizon, see [[Geocode]] description.
* In addition geological data benefit from an age scale. Please give the age of the sample (not mineral) in [ka] as additional column. You may give additional the age in Ma.
* In addition, provide sample labels and IGSN, if available

Parameter

2024-08-02T08:25:28Z

Awittmann: Corrected typos

Data submissions are required to use '''parameters''', as defined in the dictionary. Parameters are always accompanied by a '''unit'''. New parameters are defined by the Editor in Chief on request.

The '''parameters''' related to a dataset are listed in the dataset [[metaheader]].

== Definition of parameters ==
Mandatory fields are '''underlined'''; unused columns and lines in import files should be deleted.
* '''Parameter Name''' contains the full name of the parameter. Parameter Name in combination with the unit must be '''unique''' in PANGAEA. Parameter names have the most important specification in the beginning, followed by all describing terms in hierarchic order. Example: when ''dissolved organic carbon'' is measured, ''carbon'' is the main parameter information, followed by ''organic'' and the description of it's condition ''dissolved'' = Parameter Name ''Carbon, organic, dissolved''. Do not use abbreviations in the parameter name. Compare the new parameter name with existing parameters and follow their syntax.
* '''Abbreviation''' or ''short name'' of the parameter; is used in the header of data sets. The Abbreviation gives a short form of the parameter name, it never contains comma. Delta notation is given by ''d'', standard deviation and standard errors are ''std dev'' and ''std e''. Example: abbreviation of the parameter ''Carbon, organic, dissolved'' is ''DOC''.
* '''Unit''' should be given for all numeric-parameters and should follow ''standard use'' i.a. already existing parameter should only be defined with an other unit if the values can not be converted from one to an other. The unit does not contain chemical formulas, elements or the sampling milieu. This must be given in the Parameter name. Text-parameters have no unit, ''delete the unit column in import form or leave empty''. Example: parameter ''Carbon, organic, dissolved'' has the unit ''µmol/kg'' not µmol C/kg.

== See also ==
* [[Data model]]


== Parameter list ==
* [https://www.pangaea.de/lists/parameter/all-byname Complete list of parameters used in PANGAEA]

Binary objects

2024-06-07T12:43:50Z

Awittmann: Added characters to avoid when naming files.

Binary files with specific formats (e.g. shape files, netCDF, segy, images, videos, ...) will be archived as links to files. For these data types submissions (even if <20 files or <100 MB), please always request an upload link during the submission - see screenshot.
[[File:Request upload link.png|alt=Screenshot from submission form: request upload link|thumb|Screenshot from submission form: request upload link]]

In addition to the data files, please prepare a '''file list''' including:
* [[Event]]
* Latitude, Longitude (coordinated universal time, UTC)
* Date/Time (ISO-format, e.g. 1954-04-07T13:34:11)
* File names including their extension. The names should not contain spaces and special symbols.

Further columns with metadata are needed/welcome (depending on the context), for example:
* Data description / File content
* Third [[geocode]], such as Elevation, Depth, etc.
* Relative X and Y coordinates, if for example only the start and the end of the survey have known absolute georeference
* Comment

Further (automatic) columns can be configured in the table by the PANGAEA editors (these do not have to be added by the authors), including:
* File size
* Character set
* Media type
* MD5 hash

=== File list templates ===

[[Media:Template binary JPG.tab|'''photos in JPG format''' (tab-separated text file)]]
[[Media:Template binary nc.tab|'''netCDF files''' (tab-separated text file)]]
[[Media:Template binary CTD raw.tab|'''raw CTD files''' (tab-separated text file)]]

== Metadata – [[Event|Events]] table ==

The Event table is not needed, when the [[Event|Events]] are already present in PANGAEA, see https://www.pangaea.de/expeditions/ for checking. For further info see [[Station lists]]. If the event information '''cannot''' be found under https://www.pangaea.de/expeditions, please provide us with a table of additional metadata, using the template below. This will give an overview of the when, where and how the data were collected:

* Event label, unique identifier of sampling time and location.
* Campaign, e.g. ship cruise ID, please read: [[Campaign]].
* Device or method used to collect a sample or (experimental) organism, please read: [[Method]].
* Date and time in ISO-format (e.g. 1954-04-07T13:34:11) as coordinated universal time (UTC), start and end date/time must be provided in separate columns.
* Latitude and longitude in decimal degrees (S and W are negative) of data collection. For transects, start and end latitude and longitude should be provided in separate columns.
* Elevation (altitude, sea bottom depth, negative below sea level) is optional. For transects, start and end elevation must be provided in separate columns.

=== Event template with further instructions===
[[Media:Event template.xlsx|'''Event template''' (xlsx file)]]

== Naming of files ==
Please '''avoid''' the following when naming your files:

* NUL, , /, :, *, ?, ", <, >, |
* special characters such as ä, ö, ü
* spaces within file names
* . or .. and control characters

== Examples of published datasets with binary objects ==
* Photos, underwater: [https://doi.pangaea.de/10.1594/PANGAEA.936188?format=html#download Purser, A et al. (2021): Seabed photographs taken along OFOS profile PS124_8-1 during POLARSTERN cruise PS124. PANGAEA, https://doi.org/10.1594/PANGAEA.936188]
* Photos, underwater, with relative coodrinates: [https://doi.pangaea.de/10.1594/PANGAEA.958362?format=html#download Anhaus, P et al. (2023): Upward-looking still images from ROV survey PS122/1_6-16 on 2019-11-05, survey 1. PANGAEA, https://doi.org/10.1594/PANGAEA.958362]
* Photos, terrestrial: [https://doi.pangaea.de/10.1594/PANGAEA.955824?format=html#download Gómez Izquierdo, D R & Quartino, M L (2023): Photographs of Potter Cove, King George Island, looking northeast towards glacier in 2023. Instituto Antártico Argentino, Buenos Aires, Argentina, PANGAEA, https://doi.org/10.1594/PANGAEA.955824]
* Tabular data with additional photos: [https://doi.pangaea.de/10.1594/PANGAEA.927181?format=html#download Sander, Let al. (2021): Properties of a subfossil oyster bed, Grab 5. PANGAEA, https://doi.org/10.1594/PANGAEA.927181]
* NetCDF files: [https://doi.pangaea.de/10.1594/PANGAEA.944101?format=html#download Mech, M et al. (2022): Microwave brightness temperature measurements during the MOSAiC-ACA Arctic airborne campaign in late summer 2020 out of Svalbard. PANGAEA, https://doi.org/10.1594/PANGAEA.944101]
* Oceanography (CTD) raw data: [https://doi.pangaea.de/10.1594/PANGAEA.957843?format=html#download Tippenhauer, S et al. (2022): Raw data of physical oceanography during RV POLARSTERN cruises PS130/1 and PS130/2. PANGAEA, https://doi.org/10.1594/PANGAEA.957843]
* Bathymetry processed data: [https://doi.pangaea.de/10.1594/PANGAEA.956742?format=html#download Steffen, Melanie et al. (2023): Multibeam bathymetry processed data (Kongsberg EM 122 transit dataset) of RV MARIA S. MERIAN during cruise MSM79/2, Atlantic Ocean. PANGAEA, https://doi.org/10.1594/PANGAEA.956742]

File:Envir sample template bio.xlsx

2023-09-20T09:58:01Z

Awittmann: Awittmann uploaded a new version of File:Envir sample template bio.xlsx

== Summary ==
This template has been created to support the comprehensive description of environmental field observations for data submissions to PANGAEA, here with focus on biological data.

File:Envir sample template bio.xlsx

2023-09-20T09:48:12Z

Awittmann: Awittmann uploaded a new version of File:Envir sample template bio.xlsx

== Summary ==
This template has been created to support the comprehensive description of environmental field observations for data submissions to PANGAEA, here with focus on biological data.

Biology

2023-07-03T13:33:34Z

Awittmann:

Please use the templates when preparing your data and first read: [[Data submission]]. The following defines frequent data types and summarizes how to prepare biological data collected in the field or laboratory for submission to PANGAEA. Please note the following:
* In addition to the biological data, the georeferenced contextual data such as conductivity, temperature and depth data ([[CTD Underway Data|CTD]]), pH value, humidity, etc. should also be submitted to and archived at PANGAEA. If these data are archived and available in open access somewhere else, please provide the DOI link in the references box of the web submission form.
* The PANGAEA record should be understandable in itself, i.e. a potential user of the data should be able to judge quality and suitability for reuse. Thus, the record should be rich in metadata.
* The title(s), [[Abstract|abstract]](s) and keywords will need to be pasted into the web interface.
* For a complete data submission, upload all of the three tables included in the templates, i.e. the events, parameters and data tables.

== Data types and templates ==

=== Field observations/biodiversity ===

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.

'''Examples:'''
* https://doi.org/10.1594/PANGAEA.946885
* https://doi.org/10.1594/PANGAEA.950504

'''Template with further instructions:'''

[https://store.pangaea.de/documentation/PANGAEA-Wiki/Templates/Envir_sample_template_230626.xlsx Template]

=== Field experiments (including e.g. mesocosm studies) ===

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.

'''Example:'''

* https://doi.pangaea.de/10.1594/PANGAEA.959575

'''Template with further instructions:'''

[https://store.pangaea.de/documentation/PANGAEA-Wiki/Templates/Field_exp_template_230626.xlsx Template]

=== Laboratory experiments (including e.g. ship-based experiments) ===

Laboratory experiments are (comparative) studies on organisms under controlled conditions set up in a land-based or ship-based laboratory. E.g. behaviour of fish larvae in response to different treatments of CO2 partial pressure.

'''Examples:'''
* https://doi.pangaea.de/10.1594/PANGAEA.957929
* https://doi.pangaea.de/10.1594/PANGAEA.959614
* https://doi.org/10.1594/PANGAEA.951078

'''Template with further instructions:'''

[https://store.pangaea.de/documentation/PANGAEA-Wiki/Templates/Lab_exp_template_230626.xlsx Template]

=== Molecular biology ===

PANGAEA does not archive molecular sequence data, but will accept related (meta)data and establish links to the [https://www.ebi.ac.uk/ena/browser/about European Nucleotide Archive] (ENA). For more information, please read: [[Molecular data in PANGAEA]].

Examples with links to accession numbers:
* https://doi.org/10.1594/PANGAEA.923271
* https://doi.org/10.1594/PANGAEA.935870

== Metadata and Data ==

=== Metadata – [[Abstract]] ===
*The abstract/description of a dataset is NOT identical to the manuscript/article abstract, please read: [[Abstract]].
*Each submitted data table requires one specific title and abstract, even if data tables are organized in a [[PANGAEA publication types|bundled publication]] with a parent record.
*Specify whether data were collected during a field campaign, a field experiment or a land-based or ship-based laboratory experiment.
* Depending on the data type, include the following information in the abstract:
{| class="wikitable"
|+
|-
!Data type!!Additional information in abstract
|-
|Data collected directly in the field ||> Characterization of conditions in the field
|-
|Experimental data from an ''in situ''/field study ||
> Experiment site

> Conditions before and during the experiment
|-
|Laboratory experiments on cultured organisms||
> Name of the laboratory

> Name of the culture(s) collection

> Time of cultivation and no. of generations before the experiment

> Culture conditions before and during the experiment
|-
|Laboratory experiments on field-collected organisms
|
> Collection site

> Name of the laboratory

> Place, time and conditions of cultivation/animal keeping before the experiment

> Culture conditions during the experiment
|}
=== Metadata – Keywords ===

Include suitable keywords, such as:
* “Laboratory experiment” ('''mandatory''' for laboratory experiments)
* “Field experiment” ('''mandatory''' for field experiments)
* “Mesocosm experiment”
* “Field observation”
* “Cultured organism”
* “Field-collected organism”
* “Ship-based”
* “Land-based”
* “Mobile laboratory”
* Collection/experiment site
* Name of laboratory or ship

=== Metadata – [[Event|Events]] table ===

This Event table gives an overview of the when, where and how a sample or (experimental) organism was collected (prior to the experiment in case of laboratory studies), please see the [https://store.pangaea.de/documentation/PANGAEA-Wiki/Templates/Envir_sample_template_230221.xlsx template] and read: [[Event]].
* Event label, unique identifier of sampling time and location.
* Campaign, e.g. ship cruise ID, please read: [[Campaign]].
* Device or method used to collect a sample or (experimental) organism, please read: [[Method]].
* For field experiments: Device is e.g. “Field experiment” or “Mesocosm experiment (MESO)”.
* Date and time in ISO-format (e.g. 1954-04-07T13:34:11) as coordinated universal time (UTC), start and end date/time must be provided in separate columns.
* Latitude and longitude in decimal degrees (S and W are negative) of sample/organism collection site or field experiment site. For transects, start and end latitude and longitude must be provided in separate columns.
* Elevation (altitude, sea bottom depth, negative below sea level) is optional. For transects, start and end elevation must be provided in separate columns.

=== Metadata – Parameter table ===

This table summarizes all variables (PANGAEA "[[parameter|parameters]]") that are included in the data table, specifies units, principal investigator(s) and the methods used to generate the data, please see the [https://store.pangaea.de/documentation/PANGAEA-Wiki/Templates/Envir_sample_template_230221.xlsx template]
* '''Parameter''' name of the measured or determined characteristic needs to be given in full, not as abbreviation.
* The parameter name may include the species name, e.g. “Mytilus edulis, wet mass“.
* The parameter name should specify whether a parameter reflects the experimental conditions/treatment or the measured variable. For treatment parameters, use the syntax "Treatment: XY" parameters, e.g., "Treatment: Temperature, water".
* '''Unit''', SI units are preferred
* '''Principal investigator''', i.e. the person responsible for the collected data, can be different for each parameter.
* Information about the '''method/devices''' used, e.g. "Conductivity meter, Mettler Toledo, SevenGo pro SG7". If no instrument is available: provide the method used to measure the parameter, e.g. "14C radioactive tracer incubation according to Zhuang et al. 2018, doi:10.1111/1462-2920.14406". Each parameter/data set column can be assigned a separate method/device. For further information on PANGAEA method/devices, see [https://wiki.pangaea.de/wiki/Method here]
* [https://www.pangaea.de/lists/parameter/all-byname Current list of parameters used in PANGAEA]

=== Data table ===

* Only one (1) variable (PANGAEA "[[parameter|parameter]]") per column, please see the [https://store.pangaea.de/documentation/PANGAEA-Wiki/Templates/Envir_sample_template_230221.xlsx template].
* The column header contains the full parameter name and unit in squared brackets.
* If data are missing, leave the cell empty (do NOT enter "NA" or "-" etc.).
* Abbreviations should be avoided or need to be explained.
* Event label (always first column) must correspond to the entries in the events table, see [[Event]].
* Experimental data must contain parameter "Type of study" (always second column). Enter "Laboratory experiment" or "Field experiment" as values, even if all data are from the same type of study.
* Include date/time of observation if they differ from time given in the Event (use parameters "Date/time" or "Date/time start", "Date/time end"). For experiments, include date/time of experiment (use parameters "Sampling date/time, experiment" or "Date/time start, experiment", "Date/time end, experiment). Start and end date/time must be provided in separate columns
* For field observations and field experiments, include latitude and longitude. For transects, start and end latitude and longitude must be provided in separate columns.
* For field observations and field experiments, depth should be included (e.g. parameters “Depth, water”, “Depth, sediment”, "Depth, water, experiment"), even if all observations are from the surface (value = 0) as these parameters also define medium in which the samples were taken. When data are from a depth range, minimum and maximum depths must be provided in separate columns.
* To indicate whether a variable represents adjusted/intended values rather than a measured value, use "Treatment: XY" parameters, e.g., "Treatment: Temperature, water".
* For experiments, you may use the experiment parameters “Time of organism in laboratory”, “Name of laboratory”, "Latitude, experiment", "Longitude, experiment"
* For studies on cultured organisms include “Culture location”, “Name of culture collection” and “Uniform resource locator/link to reference” for a link to the culture collection.
* Spell-check all [[taxon]]<nowiki/>omic terms, e.g. by using the taxon match tools by the World Register of Marine Species ([http://www.marinespecies.org/aphia.php?p=match WoRMS]) or [https://www.lifewatch.be/data-services/ LifeWatch].
* For taxonomic terms in the data matrix, include e.g. the column "Species, unique identification" for the scientific name of the species even if only one species was studied. Please provide a [https://en.wikipedia.org/wiki/LSID Life Science Identifier] (LSID e.g. <nowiki>urn:lsid:marinespecies.org:taxname:140656</nowiki>) in a separate column, e.g. “Species, unique identification (Semantic URI)”. We recommend to use [https://www.marinespecies.org/index.php WoRMS] LSIDs for marine organisms or [https://www.itis.gov/ Integrated Taxonomic Information System] (ITIS) LSIDs for terrestrial and limnic organisms.
* For a link to e.g. [[Molecular data in PANGAEA|genetic data]], include the column "Accession number, genetics", and enter e.g. NCBI/ENA accession numbers as values.

== Frequently asked questions ==

=== Laboratory experiments ===
'''Do I need to provide georeferences for the sampling site of organisms that have been cultured or bred in the laboratory for many generations?'''

Yes, we encourage you to provide as much detail as possible on the origin of the organisms used in your laboratory study, especially if your study is relevant to the environmental sciences. Reproducibility of results depends on the laboratory strain used and the study location. The more (exact and structured) information we provide, the easier it is to decide on the suitability for reuse of the data. Please provide an events table as part of your submission. However, we are aware that for some laboratory model organisms it is close to impossible to track down the sampling event. In this case the strain(s) and culturing conditions need to be clearly described in the abstract.

Provide exact georeferences for the origin of laboratory strains in the events table and give details on strain(s) and culturing conditions in the abstract for studies like this:

* Gebühr, C., Sheward, R. M., Herrle, J. O., & Bollmann, J. (2021). Strain-specific morphological response of the dominant calcifying phytoplankton species ''Emiliania huxleyi'' to salinity change. ''PloS one'', ''16''(2), e0246745. https://doi.org/10.1371/journal.pone.0246745

Include details on strain(s) and breeding conditions in the abstract for studies like this:

* von Kortzfleisch, V. T., Karp, N. A., Palme, R., Kaiser, S., Sachser, N., & Richter, S. H. (2020). Improving reproducibility in animal research by splitting the study population into several 'mini-experiments'. ''Scientific reports'', ''10''(1), 16579. https://doi.org/10.1038/s41598-020-73503-4

Term-related taxonomic parameters

2023-06-26T09:39:47Z

Awittmann: Awittmann moved page Term-related taxonomic parameters to Intern:Term-related taxonomic parameters: internal site

#REDIRECT [[Intern:Term-related taxonomic parameters]]

Biology

2023-06-26T08:00:58Z

Awittmann: Update from Talk

Please use the templates when preparing your data and first read: [[Data submission]]. The following defines frequent data types and summarizes how to prepare biological data collected in the field or laboratory for submission to PANGAEA. Please note the following:
* In addition to the biological data, the georeferenced contextual data such as conductivity, temperature and depth data ([[CTD Underway Data|CTD]]), pH value, humidity, etc. should also be submitted to and archived at PANGAEA. If these data are archived and available in open access somewhere else, please provide the DOI link in the references box of the web submission form.
* The PANGAEA record should be understandable in itself, i.e. a potential user of the data should be able to judge quality and suitability for reuse. Thus, the record should be rich in metadata.
* The title(s), [[Abstract|abstract]](s) and keywords will need to be pasted into the web interface.
* For a complete data submission, upload all of the three tables included in the templates, i.e. the events, parameters and data tables.

== Data types and templates ==

=== Field observations/biodiversity ===

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.

'''Examples:'''
* https://doi.org/10.1594/PANGAEA.946885
* https://doi.org/10.1594/PANGAEA.950504

'''Template with further instructions:'''

[https://store.pangaea.de/documentation/PANGAEA-Wiki/Templates/Envir_sample_template_230626.xlsx Template]

=== Field experiments (including e.g. mesocosm studies) ===

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.

'''Example:'''

* https://doi.pangaea.de/10.1594/PANGAEA.959575

'''Template with further instructions:'''

[https://store.pangaea.de/documentation/PANGAEA-Wiki/Templates/Field_exp_template_230626.xlsx Template]

=== Laboratory experiments (including e.g. ship-based experiments) ===

Laboratory experiments are (comparative) studies on organisms under controlled conditions set up in a land-based or ship-based laboratory. E.g. behaviour of fish larvae in response to different treatments of CO2 partial pressure.

'''Examples:'''
* https://doi.pangaea.de/10.1594/PANGAEA.957929
* https://doi.pangaea.de/10.1594/PANGAEA.959614
* https://doi.org/10.1594/PANGAEA.951078

'''Template with further instructions:'''

[https://store.pangaea.de/documentation/PANGAEA-Wiki/Templates/Lab_exp_template_230626.xlsx Template]

=== Molecular biology ===

PANGAEA does not archive molecular sequence data, but will accept related (meta)data and establish links to the [https://www.ebi.ac.uk/ena/browser/about European Nucleotide Archive] (ENA). For more information, please read: [[Molecular data in PANGAEA]].

Examples with links to accession numbers:
* https://doi.org/10.1594/PANGAEA.923271
* https://doi.org/10.1594/PANGAEA.935870

== Metadata and Data ==

=== Metadata – [[Abstract]] ===
*The abstract/description of a dataset is NOT identical to the manuscript/article abstract, please read: [[Abstract]].
*Each submitted data table requires one abstract, even if data tables are organized in a [[PANGAEA publication types|bundled publication]] with a parent record.
*Specify whether data were collected during a field campaign, a field experiment or a land-based or ship-based laboratory experiment.
* Depending on the data type, include the following information in the abstract:
{| class="wikitable"
|+
|-
!Data type!!Additional information in abstract
|-
|Data collected directly in the field ||> Characterization of conditions in the field
|-
|Experimental data from an ''in situ''/field study ||
> Experiment site

> Conditions before and during the experiment
|-
|Laboratory experiments on cultured organisms||
> Name of the laboratory

> Name of the culture(s) collection

> Time of cultivation and no. of generations before the experiment

> Culture conditions before and during the experiment
|-
|Laboratory experiments on field-collected organisms
|
> Collection site

> Name of the laboratory

> Place, time and conditions of cultivation/animal keeping before the experiment

> Culture conditions during the experiment
|}
=== Metadata – Keywords ===

Include suitable keywords, such as:
* “Laboratory experiment” ('''mandatory''' for laboratory experiments)
* “Field experiment” ('''mandatory''' for field experiments)
* “Mesocosm experiment”
* “Field observation”
* “Cultured organism”
* “Field-collected organism”
* “Ship-based”
* “Land-based”
* “Mobile laboratory”
* Collection/experiment site
* Name of laboratory or ship

=== Metadata – [[Event|Events]] table ===

This Event table gives an overview of the when, where and how a sample or (experimental) organism was collected (prior to the experiment in case of laboratory studies), please see the [https://store.pangaea.de/documentation/PANGAEA-Wiki/Templates/Envir_sample_template_230221.xlsx template] and read: [[Event]].
* Event label, unique identifier of sampling time and location.
* Campaign, e.g. ship cruise ID, please read: [[Campaign]].
* Device or method used to collect a sample or (experimental) organism, please read: [[Method]].
* For field experiments: Device is e.g. “Field experiment” or “Mesocosm experiment (MESO)”.
* Date and time in ISO-format (e.g. 1954-04-07T13:34:11) as coordinated universal time (UTC), start and end date/time must be provided in separate columns.
* Latitude and longitude in decimal degrees (S and W are negative) of sample/organism collection site or field experiment site. For transects, start and end latitude and longitude must be provided in separate columns.
* Elevation (altitude, sea bottom depth, negative below sea level) is optional. For transects, start and end elevation must be provided in separate columns.

=== Metadata – Parameter table ===

This table summarizes all variables (PANGAEA "[[parameter|parameters]]") that are included in the data table, specifies units, principal investigator(s) and the methods used to generate the data, please see the [https://store.pangaea.de/documentation/PANGAEA-Wiki/Templates/Envir_sample_template_230221.xlsx template]
* '''Parameter''' name of the measured or determined characteristic needs to be given in full, not as abbreviation.
* The parameter name may include the species name, e.g. “Mytilus edulis, wet mass“.
* The parameter name should specify whether a parameter reflects the experimental conditions/treatment or the measured variable. For treatment parameters, use the syntax "Treatment: XY" parameters, e.g., "Treatment: Temperature, water".
* '''Unit''', SI units are preferred
* '''Principal investigator''', i.e. the person responsible for the collected data, can be different for each parameter.
* Information about the '''method/devices''' used, e.g. "Conductivity meter, Mettler Toledo, SevenGo pro SG7". If no instrument is available: provide the method used to measure the parameter, e.g. "14C radioactive tracer incubation according to Zhuang et al. 2018, doi:10.1111/1462-2920.14406". Each parameter/data set column can be assigned a separate method/device. For further information on PANGAEA method/devices, see [https://wiki.pangaea.de/wiki/Method here]
* [https://www.pangaea.de/lists/parameter/all-byname Current list of parameters used in PANGAEA]

=== Data table ===

* Only one (1) variable (PANGAEA "[[parameter|parameter]]") per column, please see the [https://store.pangaea.de/documentation/PANGAEA-Wiki/Templates/Envir_sample_template_230221.xlsx template].
* The column header contains the full parameter name and unit in squared brackets.
* If data are missing, leave the cell empty (do NOT enter "NA" or "-" etc.).
* Abbreviations should be avoided or need to be explained.
* Event label (always first column) must correspond to the entries in the events table, see [[Event]].
* Experimental data must contain parameter "Type of study" (always second column). Enter "Laboratory experiment" or "Field experiment" as values, even if all data are from the same type of study.
* Include date/time of observation if they differ from time given in the Event (use parameters "Date/time" or "Date/time start", "Date/time end"). For experiments, include date/time of experiment (use parameters "Sampling date/time, experiment" or "Date/time start, experiment", "Date/time end, experiment). Start and end date/time must be provided in separate columns
* For field observations and field experiments, include latitude and longitude. For transects, start and end latitude and longitude must be provided in separate columns.
* For field observations and field experiments, depth should be included (e.g. parameters “Depth, water”, “Depth, sediment”, "Depth, water, experiment"), even if all observations are from the surface (value = 0) as these parameters also define medium in which the samples were taken. When data are from a depth range, minimum and maximum depths must be provided in separate columns.
* To indicate whether a variable represents adjusted/intended values rather than a measured value, use "Treatment: XY" parameters, e.g., "Treatment: Temperature, water".
* For experiments, you may use the experiment parameters “Time of organism in laboratory”, “Name of laboratory”, "Latitude, experiment", "Longitude, experiment"
* For studies on cultured organisms include “Culture location”, “Name of culture collection” and “Uniform resource locator/link to reference” for a link to the culture collection.
* Spell-check all [[taxon]]<nowiki/>omic terms, e.g. by using the taxon match tools by the World Register of Marine Species ([http://www.marinespecies.org/aphia.php?p=match WoRMS]) or [https://www.lifewatch.be/data-services/ LifeWatch].
* For taxonomic terms in the data matrix, include e.g. the column "Species, unique identification" for the scientific name of the species even if only one species was studied. Please provide a [https://en.wikipedia.org/wiki/LSID Life Science Identifier] (LSID e.g. <nowiki>urn:lsid:marinespecies.org:taxname:140656</nowiki>) in a separate column, e.g. “Species, unique identification (Semantic URI)”. We recommend to use [https://www.marinespecies.org/index.php WoRMS] LSIDs for marine organisms or [https://www.itis.gov/ Integrated Taxonomic Information System] (ITIS) LSIDs for terrestrial and limnic organisms.
* For a link to e.g. [[Molecular data in PANGAEA|genetic data]], include the column "Accession number, genetics", and enter e.g. NCBI/ENA accession numbers as values.

== Frequently asked questions ==

=== Laboratory experiments ===
'''Do I need to provide georeferences for the sampling site of organisms that have been cultured or bred in the laboratory for many generations?'''

Yes, we encourage you to provide as much detail as possible on the origin of the organisms used in your laboratory study, especially if your study is relevant to the environmental sciences. Reproducibility of results depends on the laboratory strain used and the study location. The more (exact and structured) information we provide, the easier it is to decide on the suitability for reuse of the data. Please provide an events table as part of your submission. However, we are aware that for some laboratory model organisms it is close to impossible to track down the sampling event. In this case the strain(s) and culturing conditions need to be clearly described in the abstract.

Provide exact georeferences for the origin of laboratory strains in the events table and give details on strain(s) and culturing conditions in the abstract for studies like this:

* Gebühr, C., Sheward, R. M., Herrle, J. O., & Bollmann, J. (2021). Strain-specific morphological response of the dominant calcifying phytoplankton species ''Emiliania huxleyi'' to salinity change. ''PloS one'', ''16''(2), e0246745. https://doi.org/10.1371/journal.pone.0246745

Include details on strain(s) and breeding conditions in the abstract for studies like this:

* von Kortzfleisch, V. T., Karp, N. A., Palme, R., Kaiser, S., Sachser, N., & Richter, S. H. (2020). Improving reproducibility in animal research by splitting the study population into several 'mini-experiments'. ''Scientific reports'', ''10''(1), 16579. https://doi.org/10.1038/s41598-020-73503-4

Term catalogue

2023-03-23T14:34:43Z

Awittmann: corrected typos

The '''PANGAEA terminology catalogue''' (synonym: feature catalogue) is a thesaurus-like “construction kit” that is integrated into the PANGAEA internal relational data management system and enables the use of controlled vocabularies in PANGAEA. The terminology catalogue consists of relationships, concepts and terminologies that can be associated with various compounds of the PANGAEA data model such as data set parameters and their units, methods and devices or event locations.

The use of terminologies increases semantic annotations of parameters and metadata, e.g. term concepts including synonyms and hierarchies are added (“is a broader term of”), terms of different terminologies are mapped (“is same as”), and the harmonization and consistency of archived data is improved (e.g. avoidance of duplicates). This makes the data more reliable and interoperable, and facilitates comprehensive data retrievals. With respect to data retrievals, the search of data is improved by automatically assigning data sets to PANGAEA “[[topic]]s”, by allowing to search for synonyms or broader terms of concepts used in data sets, and by allowing for filtering search results ("facetting") by using the broader term relations. This way, data sets can be found even if search terms do not exactly match with the metadata of a dataset.

The PANGAEA terminology catalogue comprises distinct PANGAEA terminologies (e.g., “Keywords, PANGAEA”, “Methods and Devices, PANGAEA”) that structure terms for which no suitable external terminology services are available. In addition, PANGAEA contains terms from a number of external terminologies that are listed below. To address limitations in mapping metadata to other formats, the terminology catalogue allows mapping PANGAEA's own terms to those from external controlled vocabularies (using an “equivalent to” relation). With [http://www.marinespecies.org/index.php WoRMS] and [https://www.ebi.ac.uk/chebi/ ChEBI], PANGAEA has for some time maintained a bidirectional workflow that includes submission of new species names and regular downloads.

== List of implemented terminology services ==

'''Taxonomy''': World Register of Marine Species [https://www.marinespecies.org/ WoRMS](including information on algae by [https://www.algaebase.org/ AlgaeBase], which is redistributed by WoRMS with permission), Integrated Taxonomic Information System [https://www.itis.gov/ ITIS]

'''Measurements''': [https://www.qudt.org/ QUDT]

'''Environmental features''': The Environment [https://sites.google.com/site/environmentontology/ EnvO]

'''Chemistry''': Chemical Entities of Biological Interest [https://www.ebi.ac.uk/chebi/ ChEBI](bidirectional workflow), [https://pubchem.ncbi.nlm.nih.gov/ PubChem]

== Current activities ==

Work is currently underway to map PANGAEA method/device terms with terms from the [https://www.bodc.ac.uk/resources/products/web_services/vocab/ BODC terminology].

== References ==
British Oceanographic Data Centre (2023) The NERC Vocabulary Server, Natural Environment Research Council. https://vocab.nerc.ac.uk

Buttigieg, P.L., Morrison, N., Smith, B. et al. (2013) The environment ontology: contextualising biological and biomedical entities. Journal of Biomedical Semantics;4:43. https://doi.org/10.1186/2041-1480-4-43

FAIRsharing.org (2023) QUDT; Quantities, Units, Dimensions and Types, https://doi.org/10.25504/FAIRsharing.d3pqw7

Guiry MD & Guiry GM (2023) AlgaeBase. World-wide electronic publication, National University of Ireland, Galway. https://www.algaebase.org

Hastings J, Owen G, Dekker A, et al. (2016) ChEBI in 2016: Improved services and an expanding collection of metabolites. Nucleic Acids Research;44(D1):D1214-D1219. https://doi.org/10.1093/nar/gkv1031

Integrated Taxonomic Information System (ITIS) (2023) www.itis.gov, CC0, https://doi.org/10.5066/F7KH0KBK

Kim S, Chen J, Cheng T, et al. (2023) PubChem 2023 update. Nucleic Acids Research;51(D1):D1373–D1380. https://doi.org/10.1093/nar/gkac956

WoRMS Editorial Board (2023) World Register of Marine Species. Available from https://www.marinespecies.org at VLIZ. https://doi.org/10.14284/170

Term catalogue

2023-03-21T14:26:39Z

Awittmann: corrected references

The '''PANGAEA terminology catalogue''' (synonym: feature catalogue) is a thesaurus-like “construction kit” that is integrated into the PANGAEA internal relational data management system and enables the use of controlled vocabularies in PANGAEA. The terminology catalogue consists of relationships, concepts and terminologies that can be associated with various compounds of the PANGAEA data model such as data set parameters and their units, methods and devices or event locations.

The use of terminologies increases semantic annotations of parameters and metadata, e.g. term concepts including synonyms and hierarchies are added (“is a broader term of”), terms of different terminologies are mapped (“is same as”), and the harmonization and consistency of archived data is improved (e.g. avoidance of duplicates). This makes the data more reliable and interoperable, and facilitates comprehensive data retrievals. With respect to data retrievals, the finding of data can, for example, be improved by assigning data sets to PANGAEA “[[topic]]s” or to other data classes. This way, related data sets can be found even if search terms do not exactly match with the metadata of a dataset.

The PANGAEA terminology catalogue comprises distinct PANGAEA terminologies (e.g., “Keywords, PANGAEA”, “Methods and Devices, PANGAEA”) that structure terms for which no suitable external terminology services are available. In addition, PANGAEA contains terms from a number of external terminologies that are listed below. To address limitations in mapping metadata to other formats, the terminology catalogue allows mapping PANGAEA's own terms to those from external controlled vocabularies (using an “equivalent to” relation). With [http://www.marinespecies.org/index.php WoRMS] and [https://www.ebi.ac.uk/chebi/ ChEBI], PANGAEA has for some time maintained a bidirectional workflow that includes submission of new species names and regular downloads.

== List of implemented terminology services ==

'''Taxonomy''': World Register of Marine Species [http://www.marinespecies.org/index.php WoRMS](including information on algae by [https://www.algaebase.org/ AlgaeBase], which is redistributed by WoRMS with permission), Integrated Taxonomic Information System [https://www.itis.gov/ ITIS]

'''Measurements''': [http://www.qudt.org/ QUDT]

'''Environmental features''': The Environment [https://sites.google.com/site/environmentontology/ EnvO]

'''Chemistry''': Chemical Entities of Biological Interest [https://www.ebi.ac.uk/chebi/ ChEBI](bidirectional workflow), [https://pubchem.ncbi.nlm.nih.gov/ PubChem]

== Current activities ==

Work is currently underway to map PANGAEA method/device terms with terms from the [https://www.bodc.ac.uk/resources/products/web_services/vocab/ BODC terminology].

== References ==
British Oceanographic Data Centre (2023) The NERC Vocabulary Server, Natural Environment Research Council. https://vocab.nerc.ac.uk

Buttigieg, P.L., Morrison, N., Smith, B. et al. (2013) The environment ontology: contextualising biological and biomedical entities. Journal of Biomedical Semantics;4:43. https://doi.org/10.1186/2041-1480-4-43

FAIRsharing.org (2023) QUDT; Quantities, Units, Dimensions and Types, https://doi.org/10.25504/FAIRsharing.d3pqw7

Guiry MD & Guiry GM (2023) AlgaeBase. World-wide electronic publication, National University of Ireland, Galway. https://www.algaebase.org

Hastings J, Owen G, Dekker A, et al. (2016) ChEBI in 2016: Improved services and an expanding collection of metabolites. Nucleic Acids Research;44(D1):D1214-D1219. https://doi.org/10.1093/nar/gkv1031

Integrated Taxonomic Information System (ITIS) (2023) www.itis.gov, CC0, https://doi.org/10.5066/F7KH0KBK

Kim S, Chen J, Cheng T, et al. (2023) PubChem 2023 update. Nucleic Acids Research;51(D1):D1373–D1380. https://doi.org/10.1093/nar/gkac956

WoRMS Editorial Board (2023) World Register of Marine Species. Available from https://www.marinespecies.org at VLIZ. https://doi.org/10.14284/170

Term catalogue

2023-03-21T14:22:54Z

Awittmann: added hyperlinks in references

The '''PANGAEA terminology catalogue''' (synonym: feature catalogue) is a thesaurus-like “construction kit” that is integrated into the PANGAEA internal relational data management system and enables the use of controlled vocabularies in PANGAEA. The terminology catalogue consists of relationships, concepts and terminologies that can be associated with various compounds of the PANGAEA data model such as data set parameters and their units, methods and devices or event locations.

The use of terminologies increases semantic annotations of parameters and metadata, e.g. term concepts including synonyms and hierarchies are added (“is a broader term of”), terms of different terminologies are mapped (“is same as”), and the harmonization and consistency of archived data is improved (e.g. avoidance of duplicates). This makes the data more reliable and interoperable, and facilitates comprehensive data retrievals. With respect to data retrievals, the finding of data can, for example, be improved by assigning data sets to PANGAEA “[[topic]]s” or to other data classes. This way, related data sets can be found even if search terms do not exactly match with the metadata of a dataset.

The PANGAEA terminology catalogue comprises distinct PANGAEA terminologies (e.g., “Keywords, PANGAEA”, “Methods and Devices, PANGAEA”) that structure terms for which no suitable external terminology services are available. In addition, PANGAEA contains terms from a number of external terminologies that are listed below. To address limitations in mapping metadata to other formats, the terminology catalogue allows mapping PANGAEA's own terms to those from external controlled vocabularies (using an “equivalent to” relation). With [http://www.marinespecies.org/index.php WoRMS] and [https://www.ebi.ac.uk/chebi/ ChEBI], PANGAEA has for some time maintained a bidirectional workflow that includes submission of new species names and regular downloads.

== List of implemented terminology services ==

'''Taxonomy''': World Register of Marine Species [http://www.marinespecies.org/index.php WoRMS](including information on algae by [https://www.algaebase.org/ AlgaeBase], which is redistributed by WoRMS with permission), Integrated Taxonomic Information System [https://www.itis.gov/ ITIS]

'''Measurements''': [http://www.qudt.org/ QUDT]

'''Environmental features''': The Environment [https://sites.google.com/site/environmentontology/ EnvO]

'''Chemistry''': Chemical Entities of Biological Interest [https://www.ebi.ac.uk/chebi/ ChEBI](bidirectional workflow), [https://pubchem.ncbi.nlm.nih.gov/ PubChem]

== Current activities ==

Work is currently underway to map PANGAEA method/device terms with terms from the [https://www.bodc.ac.uk/resources/products/web_services/vocab/ BODC terminology].

== References ==
Ahyong S, Boyko CB, Bailly N, et al. (2023). World Register of Marine Species. Available from https://www.marinespecies.org at VLIZ. https://doi.org/10.14284/170

British Oceanographic Data Centre (2023). The NERC Vocabulary Server, Natural Environment Research Council. https://vocab.nerc.ac.uk

Buttigieg, P.L., Morrison, N., Smith, B. et al. (2013) The environment ontology: contextualising biological and biomedical entities. Journal of Biomedical Semantics;4:43. https://doi.org/10.1186/2041-1480-4-43

FAIRsharing.org (2023) QUDT; Quantities, Units, Dimensions and Types, https://doi.org/10.25504/FAIRsharing.d3pqw7

Guiry MD & Guiry GM (2023) AlgaeBase. World-wide electronic publication, National University of Ireland, Galway. https://www.algaebase.org

Hastings J, Owen G, Dekker A, et al. (2016) ChEBI in 2016: Improved services and an expanding collection of metabolites. Nucleic Acids Research;44(D1):D1214-D1219. https://doi.org/10.1093/nar/gkv1031

Integrated Taxonomic Information System (ITIS), www.itis.gov, CC0, https://doi.org/10.5066/F7KH0KBK

Kim S, Chen J, Cheng T, et al. (2023) PubChem 2023 update. Nucleic Acids Research;51(D1):D1373–D1380. https://doi.org/10.1093/nar/gkac956

Term catalogue

2023-03-21T14:20:13Z

Awittmann: added info on AlgaeBase, added references

The '''PANGAEA terminology catalogue''' (synonym: feature catalogue) is a thesaurus-like “construction kit” that is integrated into the PANGAEA internal relational data management system and enables the use of controlled vocabularies in PANGAEA. The terminology catalogue consists of relationships, concepts and terminologies that can be associated with various compounds of the PANGAEA data model such as data set parameters and their units, methods and devices or event locations.

The use of terminologies increases semantic annotations of parameters and metadata, e.g. term concepts including synonyms and hierarchies are added (“is a broader term of”), terms of different terminologies are mapped (“is same as”), and the harmonization and consistency of archived data is improved (e.g. avoidance of duplicates). This makes the data more reliable and interoperable, and facilitates comprehensive data retrievals. With respect to data retrievals, the finding of data can, for example, be improved by assigning data sets to PANGAEA “[[topic]]s” or to other data classes. This way, related data sets can be found even if search terms do not exactly match with the metadata of a dataset.

The PANGAEA terminology catalogue comprises distinct PANGAEA terminologies (e.g., “Keywords, PANGAEA”, “Methods and Devices, PANGAEA”) that structure terms for which no suitable external terminology services are available. In addition, PANGAEA contains terms from a number of external terminologies that are listed below. To address limitations in mapping metadata to other formats, the terminology catalogue allows mapping PANGAEA's own terms to those from external controlled vocabularies (using an “equivalent to” relation). With [http://www.marinespecies.org/index.php WoRMS] and [https://www.ebi.ac.uk/chebi/ ChEBI], PANGAEA has for some time maintained a bidirectional workflow that includes submission of new species names and regular downloads.

== List of implemented terminology services ==

'''Taxonomy''': World Register of Marine Species [http://www.marinespecies.org/index.php WoRMS](including information on algae by [https://www.algaebase.org/ AlgaeBase], which is redistributed by WoRMS with permission), Integrated Taxonomic Information System [https://www.itis.gov/ ITIS]

'''Measurements''': [http://www.qudt.org/ QUDT]

'''Environmental features''': The Environment [https://sites.google.com/site/environmentontology/ EnvO]

'''Chemistry''': Chemical Entities of Biological Interest [https://www.ebi.ac.uk/chebi/ ChEBI](bidirectional workflow), [https://pubchem.ncbi.nlm.nih.gov/ PubChem]

== Current activities ==

Work is currently underway to map PANGAEA method/device terms with terms from the [https://www.bodc.ac.uk/resources/products/web_services/vocab/ BODC terminology].

== References ==
Ahyong S, Boyko CB, Bailly N, et al. (2023). World Register of Marine Species. Available from <nowiki>https://www.marinespecies.org</nowiki> at VLIZ. <nowiki>https://doi.org/10.14284/170</nowiki>

British Oceanographic Data Centre (2023). The NERC Vocabulary Server, Natural Environment Research Council. <nowiki>https://vocab.nerc.ac.uk</nowiki>

Buttigieg, P.L., Morrison, N., Smith, B. et al. (2013) The environment ontology: contextualising biological and biomedical entities. Journal of Biomedical Semantics;4:43. <nowiki>https://doi.org/10.1186/2041-1480-4-43</nowiki>

FAIRsharing.org (2023) QUDT; Quantities, Units, Dimensions and Types, <nowiki>https://doi.org/10.25504/FAIRsharing.d3pqw7</nowiki>

Guiry MD & Guiry GM (2023) AlgaeBase. World-wide electronic publication, National University of Ireland, Galway. <nowiki>https://www.algaebase.org</nowiki>

Hastings J, Owen G, Dekker A, et al. (2016) ChEBI in 2016: Improved services and an expanding collection of metabolites. Nucleic Acids Research;44(D1):D1214-D1219. <nowiki>https://doi.org/10.1093/nar/gkv1031</nowiki>

Integrated Taxonomic Information System (ITIS), www.itis.gov, CC0, <nowiki>https://doi.org/10.5066/F7KH0KBK</nowiki>
Kim S, Chen J, Cheng T, et al. (2023) PubChem 2023 update. Nucleic Acids Research;51(D1):D1373–D1380. <nowiki>https://doi.org/10.1093/nar/gkac956</nowiki>

Biology

2023-02-21T16:24:58Z

Awittmann: Updated info on LSIDs.

Please use the templates when preparing your data and first read: [[Data submission]]. The following defines frequent data types and summarizes how to prepare biological data collected in the field or laboratory for submission to PANGAEA. Please note the following:
* In addition to the biological data, the georeferenced contextual data such as conductivity, temperature and depth data ([[CTD Underway Data|CTD]]), pH value, humidity, etc. should also be submitted to and archived at PANGAEA. If these data are archived and available in open access somewhere else, please provide the DOI link in the references box of the web submission form.
* The PANGAEA record should be understandable in itself, i.e. a potential user of the data should be able to judge quality and suitability for reuse. Thus, the record should be rich in metadata.
* The title(s), abstract(s) and keywords will need to be pasted into the web interface.
* For a complete data submission, upload all of the three tables included in the templates, i.e. the events, parameters and data tables.

== Data types and templates ==

=== Field observations/biodiversity ===

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.

Examples:
* https://doi.org/10.1594/PANGAEA.911931
* https://doi.org/10.1594/PANGAEA.917698

[https://store.pangaea.de/documentation/PANGAEA-Wiki/Templates/Envir_sample_template_230221.xlsx Template]

=== Field experiments (including e.g. mesocosm studies) ===

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.

Example:
* https://doi.org/10.1594/PANGAEA.910350

[https://store.pangaea.de/documentation/PANGAEA-Wiki/Templates/Field_exp_template_230221.xlsx Template]

=== Laboratory experiments (including e.g. ship-based experiments) ===

Laboratory experiments are (comparative) studies on organisms under controlled conditions set up in a land-based or ship-based laboratory. E.g. behaviour of fish larvae in response to different treatments of CO2 partial pressure.

Examples:
* https://doi.org/10.1594/PANGAEA.874856
* https://doi.org/10.1594/PANGAEA.951078
* https://doi.org/10.1594/PANGAEA.924440

[https://store.pangaea.de/documentation/PANGAEA-Wiki/Templates/Lab_exp_template_230221.xlsx Template]

=== Molecular biology ===

PANGAEA does not archive molecular sequence data, but will accept related (meta)data and establish links to the [https://www.ebi.ac.uk/ena/browser/about European Nucleotide Archive] (ENA). For more information, please read: [[Molecular data in PANGAEA]].

Example with links to accession numbers:
* https://doi.org/10.1594/PANGAEA.923271

== Metadata and Data ==

=== Metadata – [[Abstract]] ===
*The abstract/description of a dataset is NOT identical to the manuscript/article abstract, please read: [[Abstract]].
*Each submitted data table requires one abstract, even if data tables are organized in a [[PANGAEA publication types|bundled publication]] with a parent record.
*Specify whether data were collected during a field campaign, a field experiment or a land-based or ship-based laboratory experiment.
* Depending on the data type, include the following information in the abstract:
{| class="wikitable"
|+
|-
!Data type!!Additional information in abstract
|-
|Data collected directly in the field ||> Characterization of conditions in the field
|-
|Experimental data from an ''in situ''/field study ||
> Experiment site

> Conditions before and during the experiment
|-
|Laboratory experiments on cultured organisms||
> Name of the laboratory

> Name of the culture(s) collection

> Time of cultivation and no. of generations before the experiment

> Culture conditions before and during the experiment
|-
|Laboratory experiments on field-collected organisms
|
> Collection site

> Name of the laboratory

> Place, time and conditions of cultivation/animal keeping before the experiment

> Culture conditions during the experiment
|}
=== Metadata – Keywords ===

Include suitable keywords, such as:
* “Field observation”
* “Field experiment”
* “Mesocosm”
* “Laboratory experiment”
* “Cultured organism”
* “Field-collected organism”
* “Ship-based”
* “Land-based”
* “Mobile laboratory”
* Collection/experiment site
* Name of laboratory or ship

=== Metadata – [[Event|Events]] table ===

This table gives an overview of the when, where and how of sample or (experimental) organism collection, please see the [https://store.pangaea.de/documentation/PANGAEA-Wiki/Templates/Envir_sample_template_230221.xlsx template] and read: [[Event]].
* Event label, unique identifier of sampling time and location.
* Campaign, e.g. ship cruise ID, please read: [[Campaign]].
* Device or method used to collect a sample or (experimental) organism, please read: [[Method]].
* For field experiments: Device is e.g. “Field experiment” or “Mesocosm experiment (MESO)”.
* Date and time in ISO-format (e.g. 1954-04-07T13:34:11) as coordinated universal time (UTC), start and end date/time must be provided in separate columns.
* Latitude and longitude in decimal degrees (S and W are negative) of sample/organism collection site or field experiment site. For transects, start and end latitude and longitude must be provided in separate columns.
* Elevation (altitude, sea bottom depth, negative below sea level) is optional. For transects, start and end elevation must be provided in separate columns.

=== Metadata – Parameter table ===

This table summarizes all the parameters included in the data table, specifies units, principal investigator(s) and the methods used to generate the data, please see the [https://store.pangaea.de/documentation/PANGAEA-Wiki/Templates/Envir_sample_template_230221.xlsx template]
* Parameter name of the measured or determined characteristic needs to be given in full, not as abbreviation.
* The parameter name may include the species name, e.g. “Mytilus edulis, wet mass“.
* The parameter name should specify when data are from an experiment, e.g. “DEPTH, water, experiment”, “Temperature, air, experiment”, “Treatment: NaCl”.
* Unit, SI units are preferred
* Principal investigator, i.e. the person responsible for the collected data can be different for each parameter.
* Method or device used to collect the data: Give instrument name and manufacturer.
* [https://www.pangaea.de/lists/parameter/all-byname Current list of parameters used in PANGAEA]

=== Data table ===

* Only one (1) parameter per column, as given in the parameter table, please see the [https://store.pangaea.de/documentation/PANGAEA-Wiki/Templates/Envir_sample_template_230221.xlsx template].
* The column header contains the full parameter name and unit in squared brackets.
* If data are missing, leave the cell empty (do NOT enter "NA" or "-" etc.).
* Abbreviations should be avoided or need to be explained.
* Event label (always first column) must correspond to the entries in the events table, see [[Event]].
* Includes date/time of observation or experiment. Start and end date/time must be provided in separate columns.
* For field observations and field experiments, include latitude and longitude. For transects, start and end latitude and longitude must be provided in separate columns.
* For field observations and field experiments, depth should be included (e.g. parameters “Depth, water”, “Depth, sediment”) , even if all observations are from the surface (value = 0). When data are from a depth range, minimum and maximum depths must be provided in separate columns.
* For experiments, include the column "Type", and enter e.g. "laboratory experiment" or "field experiment" as values, even if all data are from the same type of study.
* For experiments, use the experiment parameters “Date of experiment”, “Time of organism in laboratory”, “Name of laboratory”.
* For studies on cultured organisms include “Culture location”, “Name of culture collection” and “Uniform resource locator/link to reference” for a link to the culture collection.
* Spell-check all [[taxon]]<nowiki/>omic terms, e.g. by using the taxon match tools by the World Register of Marine Species ([http://www.marinespecies.org/aphia.php?p=match WoRMS]) or [https://www.lifewatch.be/data-services/ LifeWatch].
* For taxonomic terms in the data matrix, include e.g. the column "Species, unique identification" for the scientific name of the species even if only one species was studied. Please provide a [https://en.wikipedia.org/wiki/LSID Life Science Identifier] (LSID e.g. <nowiki>urn:lsid:marinespecies.org:taxname:140656</nowiki>) in a separate column, e.g. “Species, unique identification (Semantic URI)”. We recommend to use [https://www.marinespecies.org/index.php WoRMS] LSIDs for marine organisms or [https://www.itis.gov/ Integrated Taxonomic Information System] (ITIS) LSIDs for terrestrial and limnic organisms.
* For a link to e.g. genetic data, include the column "Accession number, genetics", and enter e.g. NCBI/ENA accession numbers as values.

== Frequently asked questions ==

=== Laboratory experiments ===
'''Do I need to provide georeferences for the sampling site of organisms that have been cultured or bred in the laboratory for many generations?'''

Yes, we encourage you to provide as much detail as possible on the origin of the organisms used in your laboratory study, especially if your study is relevant to the environmental sciences. Reproducibility of results depends on the laboratory strain used and the study location. The more (exact and structured) information we provide, the easier it is to decide on the suitability for reuse of the data. Please provide an events table as part of your submission. However, we are aware that for some laboratory model organisms it is close to impossible to track down the sampling event. In this case the strain(s) and culturing conditions need to be clearly described in the abstract.

Provide exact georeferences for the origin of laboratory strains in the events table and give details on strain(s) and culturing conditions in the abstract for studies like this:

* Gebühr, C., Sheward, R. M., Herrle, J. O., & Bollmann, J. (2021). Strain-specific morphological response of the dominant calcifying phytoplankton species ''Emiliania huxleyi'' to salinity change. ''PloS one'', ''16''(2), e0246745. https://doi.org/10.1371/journal.pone.0246745

Include details on strain(s) and breeding conditions in the abstract for studies like this:

* von Kortzfleisch, V. T., Karp, N. A., Palme, R., Kaiser, S., Sachser, N., & Richter, S. H. (2020). Improving reproducibility in animal research by splitting the study population into several 'mini-experiments'. ''Scientific reports'', ''10''(1), 16579. https://doi.org/10.1038/s41598-020-73503-4

Biology

2023-02-21T15:58:23Z

Awittmann: Updated templates

Please use the templates when preparing your data and first read: [[Data submission]]. The following defines frequent data types and summarizes how to prepare biological data collected in the field or laboratory for submission to PANGAEA. Please note the following:
* In addition to the biological data, the georeferenced contextual data such as conductivity, temperature and depth data ([[CTD Underway Data|CTD]]), pH value, humidity, etc. should also be submitted to and archived at PANGAEA. If these data are archived and available in open access somewhere else, please provide the DOI link in the references box of the web submission form.
* The PANGAEA record should be understandable in itself, i.e. a potential user of the data should be able to judge quality and suitability for reuse. Thus, the record should be rich in metadata.
* The title(s), abstract(s) and keywords will need to be pasted into the web interface.
* For a complete data submission, upload all of the three tables included in the templates, i.e. the events, parameters and data tables.

== Data types and templates ==

=== Field observations/biodiversity ===

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.

Examples:
* https://doi.org/10.1594/PANGAEA.911931
* https://doi.org/10.1594/PANGAEA.917698

[https://store.pangaea.de/documentation/PANGAEA-Wiki/Templates/Envir_sample_template_230221.xlsx Template]

=== Field experiments (including e.g. mesocosm studies) ===

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.

Example:
* https://doi.org/10.1594/PANGAEA.910350

[https://store.pangaea.de/documentation/PANGAEA-Wiki/Templates/Field_exp_template_230221.xlsx Template]

=== Laboratory experiments (including e.g. ship-based experiments) ===

Laboratory experiments are (comparative) studies on organisms under controlled conditions set up in a land-based or ship-based laboratory. E.g. behaviour of fish larvae in response to different treatments of CO2 partial pressure.

Examples:
* https://doi.org/10.1594/PANGAEA.874856
* https://doi.org/10.1594/PANGAEA.951078
* https://doi.org/10.1594/PANGAEA.924440

[https://store.pangaea.de/documentation/PANGAEA-Wiki/Templates/Lab_exp_template_230221.xlsx Template]

=== Molecular biology ===

PANGAEA does not archive molecular sequence data, but will accept related (meta)data and establish links to the [https://www.ebi.ac.uk/ena/browser/about European Nucleotide Archive] (ENA). For more information, please read: [[Molecular data in PANGAEA]].

Example with links to accession numbers:
* https://doi.org/10.1594/PANGAEA.923271

== Metadata and Data ==

=== Metadata – [[Abstract]] ===
*The abstract/description of a dataset is NOT identical to the manuscript/article abstract, please read: [[Abstract]].
*Each submitted data table requires one abstract, even if data tables are organized in a [[PANGAEA publication types|bundled publication]] with a parent record.
*Specify whether data were collected during a field campaign, a field experiment or a land-based or ship-based laboratory experiment.
* Depending on the data type, include the following information in the abstract:
{| class="wikitable"
|+
|-
!Data type!!Additional information in abstract
|-
|Data collected directly in the field ||> Characterization of conditions in the field
|-
|Experimental data from an ''in situ''/field study ||
> Experiment site

> Conditions before and during the experiment
|-
|Laboratory experiments on cultured organisms||
> Name of the laboratory

> Name of the culture(s) collection

> Time of cultivation and no. of generations before the experiment

> Culture conditions before and during the experiment
|-
|Laboratory experiments on field-collected organisms
|
> Collection site

> Name of the laboratory

> Place, time and conditions of cultivation/animal keeping before the experiment

> Culture conditions during the experiment
|}
=== Metadata – Keywords ===

Include suitable keywords, such as:
* “Field observation”
* “Field experiment”
* “Mesocosm”
* “Laboratory experiment”
* “Cultured organism”
* “Field-collected organism”
* “Ship-based”
* “Land-based”
* “Mobile laboratory”
* Collection/experiment site
* Name of laboratory or ship

=== Metadata – [[Event|Events]] table ===

This table gives an overview of the when, where and how of sample or (experimental) organism collection, please see the [https://store.pangaea.de/documentation/PANGAEA-Wiki/Templates/Envir_sample_template_210715.xlsx template] and read: [[Event]].
* Event label, unique identifier of sampling time and location.
* Campaign, e.g. ship cruise ID, please read: [[Campaign]].
* Device or method used to collect a sample or (experimental) organism, please read: [[Method]].
* For field experiments: Device is e.g. “Field experiment” or “Mesocosm experiment (MESO)”.
* Date and time in ISO-format (e.g. 1954-04-07T13:34:11) as coordinated universal time (UTC), start and end date/time must be provided in separate columns.
* Latitude and longitude in decimal degrees (S and W are negative) of sample/organism collection site or field experiment site. For transects, start and end latitude and longitude must be provided in separate columns.
* Elevation (altitude, sea bottom depth, negative below sea level) is optional. For transects, start and end elevation must be provided in separate columns.

=== Metadata – Parameter table ===

This table summarizes all the parameters included in the data table, specifies units, principal investigator(s) and the methods used to generate the data, please see the [https://store.pangaea.de/documentation/PANGAEA-Wiki/Templates/Envir_sample_template_210715.xlsx template]
* Parameter name of the measured or determined characteristic needs to be given in full, not as abbreviation.
* The parameter name may include the species name, e.g. “Mytilus edulis, wet mass“.
* The parameter name should specify when data are from an experiment, e.g. “DEPTH, water, experiment”, “Temperature, air, experiment”, “Treatment: NaCl”.
* Unit, SI units are preferred
* Principal investigator, i.e. the person responsible for the collected data can be different for each parameter.
* Method or device used to collect the data: Give instrument name and manufacturer.
* [https://www.pangaea.de/lists/parameter/all-byname Current list of parameters used in PANGAEA]

=== Data table ===

* Only one (1) parameter per column, as given in the parameter table, please see the [https://store.pangaea.de/documentation/PANGAEA-Wiki/Templates/Envir_sample_template_210715.xlsx template].
* The column header contains the full parameter name and unit in squared brackets.
* If data are missing, leave the cell empty (do NOT enter "NA" or "-" etc.).
* Abbreviations should be avoided or need to be explained.
* Spell-check all [[taxon]]<nowiki/>omic terms, e.g. by using the taxon match tools by [http://www.marinespecies.org/aphia.php?p=match WoRMS] or [https://www.lifewatch.be/data-services/ LifeWatch].
* Event label (always first column) must correspond to the entries in the events table, see [[Event]].
* Includes date/time of observation or experiment. Start and end date/time must be provided in separate columns.
* For field observations and field experiments, include latitude and longitude. For transects, start and end latitude and longitude must be provided in separate columns.
* For field observations and field experiments, depth should be included (e.g. parameters “Depth, water”, “Depth, sediment”) , even if all observations are from the surface (value = 0). When data are from a depth range, minimum and maximum depths must be provided in separate columns.
* For experiments, include the column "Type", and enter e.g. "laboratory experiment" or "field experiment" as values, even if all data are from the same type of study.
* For experiments, use the experiment parameters “Date of experiment”, “Time of organism in laboratory”, “Name of laboratory”.
* For studies on cultured organisms include “Culture location”, “Name of culture collection” and “Uniform resource locator/link to reference” for a link to the culture collection.
* Include the column "Species", even if only one species was studied, and “Uniform resource locator/link to reference” for WoRMS species AphiaIDs.
* For a link to e.g. genetic data, include the column "Accession number, genetics", and enter e.g. NCBI/ENA accession numbers as values.

== Frequently asked questions ==

=== Laboratory experiments ===
'''Do I need to provide georeferences for the sampling site of organisms that have been cultured or bred in the laboratory for many generations?'''

Yes, we encourage you to provide as much detail as possible on the origin of the organisms used in your laboratory study, especially if your study is relevant to the environmental sciences. Reproducibility of results depends on the laboratory strain used and the study location. The more (exact and structured) information we provide, the easier it is to decide on the suitability for reuse of the data. Please provide an events table as part of your submission. However, we are aware that for some laboratory model organisms it is close to impossible to track down the sampling event. In this case the strain(s) and culturing conditions need to be clearly described in the abstract.

Provide exact georeferences for the origin of laboratory strains in the events table and give details on strain(s) and culturing conditions in the abstract for studies like this:

* Gebühr, C., Sheward, R. M., Herrle, J. O., & Bollmann, J. (2021). Strain-specific morphological response of the dominant calcifying phytoplankton species ''Emiliania huxleyi'' to salinity change. ''PloS one'', ''16''(2), e0246745. https://doi.org/10.1371/journal.pone.0246745

Include details on strain(s) and breeding conditions in the abstract for studies like this:

* von Kortzfleisch, V. T., Karp, N. A., Palme, R., Kaiser, S., Sachser, N., & Richter, S. H. (2020). Improving reproducibility in animal research by splitting the study population into several 'mini-experiments'. ''Scientific reports'', ''10''(1), 16579. https://doi.org/10.1038/s41598-020-73503-4