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Data structure

Data is presented in four tab-delimited files each corresponding to a table in a simple relational-style “database”:

Table schema diagram

Further explanation of each table can be found in the following sections, and a schema (in DBML format, the source of the diagram above) is also available.

Attribute List

Sites

Site name

name  sites.site_name
type  character

The (locally unique) identifier used by the science team which took the core. Normalised to alphanumeric characters and underscores (e.g. PO200/10_8-2.97 becomes PO200_10_8_2_97)

Latitude and longitude

name  sites.lat
type  decimal

name  sites.lon
type  decimal

lat and lon are given in decimal degrees using negative numbers for the western and southern hemispheres (i.e. the international date line is at ±180°).

Water depth

name  sites.water_depth
type  integer

Depth below mean sea level, to the nearest meter, of the seabed at the cored location.

Ocean basin

name  sites.ocean_basin
type  ocean_basin (enum)

Map of the ocean basin areas

Populated approximately according to the definitions of the International Association for the Physical Sciences of the Oceans (PDF), with additional bounds defined where implied in the original:

Code Description North East South West
NEAt Northeast Atlantic Ocean 66.5 20.0 23.5 -40.0
Med Mediterranean Sea 48.0 45.0 30.0 -5.8
NWAt Northwest Atlantic Ocean 66.5 -40.0 23.5 -100.0
TAt Tropical Atlantic Ocean 23.5 20.0 -23.5 -70.0
SAt South Atlantic Ocean -23.5 20.0 -55.0 -70.0
NEPa Northeast Pacific Ocean 66.5 -100.0 23.5 -180.0
NWPa Northwest Pacific Ocean 66.5 180.0 23.5 120.0
TPa Tropical Pacific Ocean 23.5 -70.0 -23.5 120.0
SPa South Pacific Ocean -23.5 -70.0 -55.0 120.0
EIn Eastern Indian Ocean 30.0 120.0 -55.0 80.0
WIn Western Indian Ocean 30.0 80.0 -55.0 20.0
ESo Eastern Southern Ocean -55.0 -160.0 -90.0 20.0
WSo Western Southern Ocean -55.0 20.0 -90.0 -160.0
Ar Arctic Ocean 90.0 180.0 66.5 -180.0

Notes:

  • The bounding latitude and longitude values above create simple rectangular boxes and do not take into account coastlines. The hatched area in the figure above shows where these boxes are ambiguous or wrong, and care should be taken in these areas
  • The Mediterranean and Black Seas are a special case since their oceanographic conditions are quite different from the Northeast Atlantic. Both are categorised as Med, the western boundary of which is taken as the Kamara Ridge, the shallowest part of the Straits of Gibraltar (see Figure 1 in de Stephanis et al., 2008). The boundaries in the above table include the Bay of Biscay but in the compilation code, this is avoided by using two boxes.
  • The other major seas are included in their parent ocean:
    • Caribbean Sea: Tropical Atlantic (TAt)
    • Gulf of Mexico: NW Atlantic (NWAt)
    • Hudson Bay: Arctic (Ar)
  • lat and lon can always be used to filter sites of interest from ambiguous areas.
  • North and west bounds are inclusive, and east and south are exclusive - for example, the arctic ocean is defined as:
  90 >= lat > 66.5;
-180 <= lon < 180;

Samples

Site name ☍

name        samples.site_name
type        character
constraint  foreign key

The same as Sites: Site name and the value for a record in this table must be present in the sites table (i.e. it is a foreign key, ☍).

Depth in core

name  samples.depth_in_core
type  decimal

The depth down-core of the sample, in meters.

Age

name  samples.age
type  decimal

The age of the sample, in thousands of years before present (kyr BP), according to the age model of the study in which the sample was published (denoted by the citekey attribute).

Taxon ID ☍

name        samples.taxon_id
type        integer
constraint  foreign key

A link to the relevant record in the taxa table. See Taxa: Taxon ID

Citekey ☍

name        samples.citekey
type        character
constraint  foreign key

A link to the relevant record in the studies table. If the data was used in more than one publication according to Jonkers et al. (2020), this refers to the first study mentioned. See Studies: Citekey

Data URL

name  samples.data_url
type  character

URL of the data, if available.

δ18O

name  samples.d18o
type  decimal

The δ18O measurement of the calcite of the taxon_id in this age interval.

δ13C

name  samples.d13c
type  decimal

The δ13C measurement of the calcite of the taxon_id in this age interval.

Taxa

Taxon ID

name        taxa.taxon_id
type        character
constraint  primary key

A locally unique code, composed of a contraction of the genus name for taxa specified to genus level, and the first letter of the genus with a contraction of the species name, separated by an underscore, for a taxon defined to species level. With or without a modifier for morphotypes etc. (see taxa.type). For example, Globigerinoides ruber (pink) has the taxon ID G_ruber_p. See also: Genus, species, type

Grouping

name  taxa.grouping
type  character

A functional grouping of similar taxa, or a grouping of taxa which were not identified to Genus or species level (for example, “various benthics”).

Genus, species, type

name  taxa.genus
type  character

name  taxa.species
type  character

name  taxa.type
type  character

The accepted binomial name of the taxon, according to the World Register of Marine Species. taxa.species may be empty if the species is uncertain or various, and the taxa.type field allows morphotypes, chromotypes, and so on:

Taxon ID Genus Species Type Example textual style
Globigrnds Globigerinoides Globigerinoides spp.
G_ruber Globigerinoides ruber G. ruber
G_ruber_p Globigerinoides ruber pink G. ruber (pink)

Habitat

name  taxa.habitat
type  habitat (enum)

A code describing the general habitat of the foraminiferal species:

Code Description
Bn Benthic
Pl Planktic

Original name

name  taxa.original_name
type  habitat (enum)

The species name as reported in the original, if different from the values in the other attributes in this table. Names may have been changed because taxa have been redefined since the original (e.g. G. sacculifer to T. sacculifer) or because they were synonyms of a taxon already present in the table (e.g. N. pachyderma sinistralis and N. pachyderma (left)).

Studies

All studies referenced in the dataset are also listed in the bibTeX file /docs/references.bib for easy import into reference managers.

Citekey

name        studies.citekey
type        character
constraint  primary key

A locally unique ID based on the JabRef key patterns in the form [auth.etal:lower][year].

Title

name  studies.title
type  character

Lead author, other authors

name  studies.lead_author
type  character

name  studies.other_authors
type  character

The names of the authors of the study in the format family_name, first_initial. [prefix] (e.g. "Einstein, A." or "Humboldt, A. von"). Other authors are separated by a semicolon and a space.

Year

name  studies.year
type  integer

The publication year for the original study.

DOI

name  studies.doi
type  character

The Digital Object Identifier of the study. Resolved at https://doi.org/<doi> where <doi> is the value of this field.

Journal

name  studies.journal
type  character

The title (name) of the Journal in which the paper was published (if applicable).

Book

name  studies.book
type  character

The title of the book in which the section or chapter was published (if applicable).

Env

This table contains modern (and eventually palaeo-) environmental data for each site listed in the sites table, useful for filtering the sites to include in any analyses.

Site name ☍

name        env.site_name
type        character
constraint  foreign key

Cross-reference to Sites: Site name.

Modern surface chlorophyll

name  env.chl_a_modern
type  decimal

The modern surface chlorophyll-a value for the 1-degree pixel in which the site is located, derived from the MODIS Aqua entire mission composite, 2002-2020