Talk:Biology

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), 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.

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

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.939970 [Type of study missing]
 * https://doi.org/10.1594/PANGAEA.947996 [Type of study missing]
 * https://doi.org/10.1594/PANGAEA.959575 [DOI reg in progress]

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.957929
 * https://doi.org/10.1594/PANGAEA.959614
 * https://doi.org/10.1594/PANGAEA.951078

Template

Molecular biology
PANGAEA does not archive molecular sequence data, but will accept related (meta)data and establish links to the 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 – 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 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:

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

Metadata – Events table
This 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 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 "parameters") that are included in the data table, specifies units, principal investigator(s) and the methods used to generate the data, please see the 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.
 * Information about the instrument/devices used, e.g. "Conductivity meter, Mettler Toledo, SevenGo pro SG7". If no instrument is available: 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. For further information, see
 * Current list of parameters used in PANGAEA

Data table

 * Only one (1) variable ("parameter") per column, please see the 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.
 * Include date/time of observation (parameter "Date/time") or date/time of experiment ("Date/time, experiment"). Start and end date/time must be provided in separate columns (observations: use parameters "Date/time start", "Date/time end"; experiments: use parameters "Date/time start, experiment", "Date/time end, experiment"). (QUestion: also date/time, experiment in field experiments? I would say yes as it shows that date/time is equal to EVENT metadata if in deed equal..) For simplicity, I would just configure Event Date/time etc into the data matrix.Bold text
 * 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, experiment") QUESTION: FIELD EXPERIMENTS: DEPTH; EXPERIMENT OR DEPTH,WATER?? -> DEPTH, water, experiment! :-), 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 of study", and enter e.g. "laboratory experiment" or "field experiment" as values, even if all data are from the same type of study.
 * 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”.
 * 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 omic terms, e.g. by using the taxon match tools by the World Register of Marine Species (WoRMS) or 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 Life Science Identifier (LSID e.g. urn:lsid:marinespecies.org:taxname:140656 ) in a separate column, e.g. “Species, unique identification (Semantic URI)”. We recommend to use WoRMS LSIDs for marine organisms or 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.

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