Phytoplankton Data Template
The Phyto VRE web services use a specific Data Template which is based on the Darwin Core standard (http://rs.tdwg.org/dwc/) and the Thesaurus of Phytoplankton Traits (http://ecoportal.lifewatch.eu/ontologies/PHYTOTRAITS).
The Data Template is a CSV UTF-8 file with semicolon delimited values that uses the point as a decimal separator. It is a column-oriented table with, in the header row, all fields related to ancillary information (e.g., country, locality, day, month, year, eventid, parenteventid, decimallatitude, decimallongitude, etc.) and phytoplankton features (e.g. phylum, class, shape, linear dimensions, biovolume, etc.).
An extensive description of each field with recommendations on how to fill in some mandatory fields is reported in Table 2.
Please note that not all fields are required for every web service. Table 1 gives an overview of the mandatory fields for each web service:
Table 1. Mandatory fields in the phytoplankton data template according to the specific web service.
Web Service | Mandatory fields in the Data Template |
Traits Computation (simplified calculation) |
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Traits Computation (advanced calculation) |
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Size Class Distribution |
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Size Abundance Relationships |
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Table 2. Detailed description of the phytoplankton data template’s fields.
Field Name | Field Description | Field URI | Field Data Type | Recommendations for filling in |
catalognumber | An identifier (preferably unique) for the record within the data set or collection. | String | ||
organismquantity | A number or enumeration value for the quantity of organisms. An organismquantity must have a corresponding organismquantitytype (e.g., "27" for organismquantity with "individuals" for organismquantitytype). | Integer | ||
organismquantitytype | The type of quantification system used for the quantity of organisms. An organismquantitytype must have a corresponding organismquantity (e.g., "27" for organismquantity with "individuals" for organismquantitytype). | String | ||
eventid | An identifier for the set of information associated with an Event (something that occurs at a place and time). May be a global unique identifier or an identifier specific to the data set. | String | ||
parentevendid | An identifier for the broader Event that groups this and potentially other Events. May be a globally unique identifier or an identifier specific to the data set (e.g. "a1" as parenteventid to identify the main whittaker plot in nested samples, each with its own eventid (e.g., "a1:1", "a1:2"). | String | ||
country | The name of the country in which the location occurs. Please select a country from iso 3166 standard (https://www.iso.org/obp/ui/#search). | String | ||
countrycode | The standard code for the country in which the Location occurs. Recommended best practice is to use ISO 3166-1-alpha-2 country codes (https://www.iso.org/obp/ui/#search). | String | ||
locality | The specific description of the place. | String | ||
decimallatitude | The geographic latitude (in decimal degrees, using the spatial reference system given in geodeticdatum) of the geographic center of a location. Positive values are north of the equator, negative values are south of it. legal values lie between -90 and 90, inclusive. | String | ||
decimallongitude | The geographic longitude (in decimal degrees, using the spatial reference system given in geodeticdatum) of the geographic center of a location. Positive values are east of the Greenwich Meridian, negative values are west of it. Legal values lie between -180 and 180, inclusive. | Double | ||
day | The integer day of the month on which the Event occurred (e.g. 1, 9, 28). | Double | ||
month | The integer month in which the Event occurred (e.g. 1 for January, 10 for October). | Integer | ||
year | The four-digit year in which the Event occurred, according to the Common Era Calendar (e.g. 1998, 2021). | Integer | ||
phylum | The full scientific name of the phylum or division in which the taxon is classified. | Integer | ||
class | The full scientific name of the class in which the taxon is classified. | String | ||
order | The full scientific name of the order in which the taxon is classified. | String | ||
family | The full scientific name of the family in which the taxon is classified. | String | ||
genus | The full scientific name of the genus in which the taxon is classified. | String | ||
providedscientificname | The full scientificname, with authorship and date information if known, with identification qualifications as it originally provided by user (e.g. Asterionellopsis cf. glacialis, Navicula sp., etc.). | NA | String | |
scientificname | The full scientific name, with authorship and date information if known. When forming part of an Identification, this should be the name in lowest level taxonomic rank that can be determined. | String | In phytoplankton data template, this field must only contain the scientific name associated to the organism without authorship, date information and all additional information that is not part of the species/taxon name (e.g. erase all notations of sp., sp. 1, spp., cfr., undet., indet., etc.) in order to match your species/taxon list with our list used in the traits computation webservice (e.g. Asterionellopsis if the original name is Asterionellopsis cf. glacialis) . All removed information can be reported in the field providedscientificname. | |
volumeofsedimentationchamber | The volume of water sample used for sedimentation expressed in milliliter. | NA | Integer | |
transectcounting | The number of counted fields or diametral transects or the surface of the sedimentation chamber. | NA | Integer | |
measurementremarks | Comments or notes accompanying the Measurement Or Fact. | String | In phytoplankton data template, measurement remarks are comments or notes about the sedimentation view of the organism (i.e. frontal, lateral, unique, valvar and girdle) and/or for some cases the approximative individual size (more than 20 micrometer, less than 20 micrometer and around 100 micrometer). This information will be used to associate the linear dimensions to the shape. | |
shape | The approximate 3 dimensional shape of a cell, described as one or more geometric solids. | String | In phytoplankton data template, this field must contain the name of shape associated to the organism following the Atlas of shape (https://www.phytovre.lifewatchitaly.eu/vre/shapes-groups/). The Atlas includes an illustrative scheme of the shape classification subdivided in “Simple Shapes” and “Complex Shapes” and the corresponding linear dimensions needed for the traits computation webservice. | |
length | A 1-D extent quality which is equal to the distance between two points expressed in micrometer and indicated by alphabetical code “a; e; l”. In particular, in complex shapes, there are more than one length identified through different alphanumerical codes "a1; a2; a3; l1; l2; l3; l4". | Double | In phytoplankton data template, this field must contain the measured value according to the Atlas of Shapes (https://www.phytovre.lifewatchitaly.eu/vre/shapes-groups/). | |
width | A 1-D extent quality which is equal to the distance from one side of an object to another side which is opposite, expressed in micrometer and i ndicated by alphabetical code “b; d ”. In particular, in complex shapes, there are more than one width identified through different alphanumerical codes "b1; b2; b3; b4; d1; d11; d2; d22; d3; d33; d4; d44". | Double | In phytoplankton data template, this field must contain the measured value according to the Atlas of Shapes (https://www.phytovre.lifewatchitaly.eu/vre/shapes-groups/). |
a | A 1-D extent quality which is equal to the distance between two points expressed in micrometer and indicated by alphabetical code “a; e; l”. In particular, in complex shapes, there are more than one length identified through different alphanumerical codes "a1; a2; a3; l1; l2; l3; l4". | Double | In phytoplankton data template, this field must contain the measured value according to the Atlas of Shapes (https://www.phytovre.lifewatchitaly.eu/vre/shapes-groups/). | |
b | A 1-D extent quality which is equal to the distance from one side of an object to another side which is opposite, expressed in micrometer and i ndicated by alphabetical code “b; d ”. In particular, in complex shapes, there are more than one width identified through different alphanumerical codes "b1; b2; b3; b4; d1; d11; d2; d22; d3; d33; d4; d44". | Double | In phytoplankton data template, this field must contain the measured value according to the Atlas of Shapes (https://www.phytovre.lifewatchitaly.eu/vre/shapes-groups/). | |
c | A 1-D extent quality which is equal to the dimension through an object as opposed to its length or width, expressed in micrometerand indicated by alphabetical code “c; h”. In particular, in complex shapes, there are more than one thickness identified through different alphanumerical codes "c1; c2; c3; h1; h2; h3; h4". | Double | In phytoplankton data template, this field must contain the measured value according to the Atlas of Shapes (https://www.phytovre.lifewatchitaly.eu/vre/shapes-groups/). | |
d | A 1-D extent quality which is equal to the distance from one side of an object to another side which is opposite, expressed in micrometer and i ndicated by alphabetical code “b; d ”. In particular, in complex shapes, there are more than one width identified through different alphanumerical codes "b1; b2; b3; b4; d1; d11; d2; d22; d3; d33; d4; d44". | Double | In phytoplankton data template, this field must contain the measured value according to the Atlas of Shapes (https://www.phytovre.lifewatchitaly.eu/vre/shapes-groups/). | |
h | A 1-D extent quality which is equal to the dimension through an object as opposed to its length or width, expressed in micrometerand indicated by alphabetical code “c; h”. In particular, in complex shapes, there are more than one thickness identified through different alphanumerical codes "c1; c2; c3; h1; h2; h3; h4". | Double | In phytoplankton data template, this field must contain the measured value according to the Atlas of Shapes (https://www.phytovre.lifewatchitaly.eu/vre/shapes-groups/). | |
a1 | A 1-D extent quality which is equal to the distance between two points expressed in micrometer and indicated by alphabetical code “a; e; l”. In particular, in complex shapes, there are more than one length identified through different alphanumerical codes "a1; a2; a3; l1; l2; l3; l4". | Double | In phytoplankton data template, this field must contain the measured value according to the Atlas of Shapes (https://www.phytovre.lifewatchitaly.eu/vre/shapes-groups/). | |
b1 | A 1-D extent quality which is equal to the distance from one side of an object to another side which is opposite, expressed in micrometer and i ndicated by alphabetical code “b; d ”. In particular, in complex shapes, there are more than one width identified through different alphanumerical codes "b1; b2; b3; b4; d1; d11; d2; d22; d3; d33; d4; d44". | Double | In phytoplankton data template, this field must contain the measured value according to the Atlas of Shapes (https://www.phytovre.lifewatchitaly.eu/vre/shapes-groups/). | |
c1 | A 1-D extent quality which is equal to the dimension through an object as opposed to its length or width, expressed in micrometerand indicated by alphabetical code “c; h”. In particular, in complex shapes, there are more than one thickness identified through different alphanumerical codes "c1; c2; c3; h1; h2; h3; h4". | Double | In phytoplankton data template, this field must contain the measured value according to the Atlas of Shapes (https://www.phytovre.lifewatchitaly.eu/vre/shapes-groups/). | |
h1 | A 1-D extent quality which is equal to the dimension through an object as opposed to its length or width, expressed in micrometerand indicated by alphabetical code “c; h”. In particular, in complex shapes, there are more than one thickness identified through different alphanumerical codes "c1; c2; c3; h1; h2; h3; h4". | Double | In phytoplankton data template, this field must contain the measured value according to the Atlas of Shapes (https://www.phytovre.lifewatchitaly.eu/vre/shapes-groups/). | |
d1 | A 1-D extent quality which is equal to the distance from one side of an object to another side which is opposite, expressed in micrometer and i ndicated by alphabetical code “b; d ”. In particular, in complex shapes, there are more than one width identified through different alphanumerical codes "b1; b2; b3; b4; d1; d11; d2; d22; d3; d33; d4; d44". | Double | In phytoplankton data template, this field must contain the measured value according to the Atlas of Shapes (https://www.phytovre.lifewatchitaly.eu/vre/shapes-groups/). | |
a2 | A 1-D extent quality which is equal to the distance between two points expressed in micrometer and indicated by alphabetical code “a; e; l”. In particular, in complex shapes, there are more than one length identified through different alphanumerical codes "a1; a2; a3; l1; l2; l3; l4". | Double | In phytoplankton data template, this field must contain the measured value according to the Atlas of Shapes (https://www.phytovre.lifewatchitaly.eu/vre/shapes-groups/). | |
b2 | A 1-D extent quality which is equal to the distance from one side of an object to another side which is opposite, expressed in micrometer and i ndicated by alphabetical code “b; d ”. In particular, in complex shapes, there are more than one width identified through different alphanumerical codes "b1; b2; b3; b4; d1; d11; d2; d22; d3; d33; d4; d44". | Double | In phytoplankton data template, this field must contain the measured value according to the Atlas of Shapes (https://www.phytovre.lifewatchitaly.eu/vre/shapes-groups/). | |
c2 | A 1-D extent quality which is equal to the dimension through an object as opposed to its length or width, expressed in micrometerand indicated by alphabetical code “c; h”. In particular, in complex shapes, there are more than one thickness identified through different alphanumerical codes "c1; c2; c3; h1; h2; h3; h4". | Double | In phytoplankton data template, this field must contain the measured value according to the Atlas of Shapes (https://www.phytovre.lifewatchitaly.eu/vre/shapes-groups/). | |
h2 | A 1-D extent quality which is equal to the dimension through an object as opposed to its length or width, expressed in micrometerand indicated by alphabetical code “c; h”. In particular, in complex shapes, there are more than one thickness identified through different alphanumerical codes "c1; c2; c3; h1; h2; h3; h4". | Double | In phytoplankton data template, this field must contain the measured value according to the Atlas of Shapes (https://www.phytovre.lifewatchitaly.eu/vre/shapes-groups/). | |
d2 | A 1-D extent quality which is equal to the distance from one side of an object to another side which is opposite, expressed in micrometer and i ndicated by alphabetical code “b; d ”. In particular, in complex shapes, there are more than one width identified through different alphanumerical codes "b1; b2; b3; b4; d1; d11; d2; d22; d3; d33; d4; d44". | Double | In phytoplankton data template, this field must contain the measured value according to the Atlas of Shapes (https://www.phytovre.lifewatchitaly.eu/vre/shapes-groups/). | |
a3 | A 1-D extent quality which is equal to the distance between two points expressed in micrometer and indicated by alphabetical code “a; e; l”. In particular, in complex shapes, there are more than one length identified through different alphanumerical codes "a1; a2; a3; l1; l2; l3; l4". | Double | In phytoplankton data template, this field must contain the measured value according to the Atlas of Shapes (https://www.phytovre.lifewatchitaly.eu/vre/shapes-groups/). | |
b3 | A 1-D extent quality which is equal to the distance from one side of an object to another side which is opposite, expressed in micrometer and i ndicated by alphabetical code “b; d ”. In particular, in complex shapes, there are more than one width identified through different alphanumerical codes "b1; b2; b3; b4; d1; d11; d2; d22; d3; d33; d4; d44". | Double | In phytoplankton data template, this field must contain the measured value according to the Atlas of Shapes (https://www.phytovre.lifewatchitaly.eu/vre/shapes-groups/). | |
c3 | A 1-D extent quality which is equal to the dimension through an object as opposed to its length or width, expressed in micrometerand indicated by alphabetical code “c; h”. In particular, in complex shapes, there are more than one thickness identified through different alphanumerical codes "c1; c2; c3; h1; h2; h3; h4". | Double | In phytoplankton data template, this field must contain the measured value according to the Atlas of Shapes (https://www.phytovre.lifewatchitaly.eu/vre/shapes-groups/). | |
h3 | A 1-D extent quality which is equal to the dimension through an object as opposed to its length or width, expressed in micrometerand indicated by alphabetical code “c; h”. In particular, in complex shapes, there are more than one thickness identified through different alphanumerical codes "c1; c2; c3; h1; h2; h3; h4". | Double | In phytoplankton data template, this field must contain the measured value according to the Atlas of Shapes (https://www.phytovre.lifewatchitaly.eu/vre/shapes-groups/). | |
d3 | A 1-D extent quality which is equal to the distance from one side of an object to another side which is opposite, expressed in micrometer and i ndicated by alphabetical code “b; d ”. In particular, in complex shapes, there are more than one width identified through different alphanumerical codes "b1; b2; b3; b4; d1; d11; d2; d22; d3; d33; d4; d44". | Double | In phytoplankton data template, this field must contain the measured value according to the Atlas of Shapes (https://www.phytovre.lifewatchitaly.eu/vre/shapes-groups/). | |
h4 | A 1-D extent quality which is equal to the dimension through an object as opposed to its length or width, expressed in micrometerand indicated by alphabetical code “c; h”. In particular, in complex shapes, there are more than one thickness identified through different alphanumerical codes "c1; c2; c3; h1; h2; h3; h4". | Double | In phytoplankton data template, this field must contain the measured value according to the Atlas of Shapes (https://www.phytovre.lifewatchitaly.eu/vre/shapes-groups/). | |
d4 | A 1-D extent quality which is equal to the distance from one side of an object to another side which is opposite, expressed in micrometer and i ndicated by alphabetical code “b; d ”. In particular, in complex shapes, there are more than one width identified through different alphanumerical codes "b1; b2; b3; b4; d1; d11; d2; d22; d3; d33; d4; d44". | Double | In phytoplankton data template, this field must contain the measured value according to the Atlas of Shapes (https://www.phytovre.lifewatchitaly.eu/vre/shapes-groups/). | |
e | A 1-D extent quality which is equal to the distance between two points expressed in micrometer and indicated by alphabetical code “a; e; l”. In particular, in complex shapes, there are more than one length identified through different alphanumerical codes "a1; a2; a3; l1; l2; l3; l4". | Double | In phytoplankton data template, this field must contain the measured value according to the Atlas of Shapes (https://www.phytovre.lifewatchitaly.eu/vre/shapes-groups/). | |
l | A 1-D extent quality which is equal to the distance between two points expressed in micrometer and indicated by alphabetical code “a; e; l”. In particular, in complex shapes, there are more than one length identified through different alphanumerical codes "a1; a2; a3; l1; l2; l3; l4". | Double | In phytoplankton data template, this field must contain the measured value according to the Atlas of Shapes (https://www.phytovre.lifewatchitaly.eu/vre/shapes-groups/). | |
l1 | A 1-D extent quality which is equal to the distance between two points expressed in micrometer and indicated by alphabetical code “a; e; l”. In particular, in complex shapes, there are more than one length identified through different alphanumerical codes "a1; a2; a3; l1; l2; l3; l4". | Double | In phytoplankton data template, this field must contain the measured value according to the Atlas of Shapes (https://www.phytovre.lifewatchitaly.eu/vre/shapes-groups/). | |
l2 | A 1-D extent quality which is equal to the distance between two points expressed in micrometer and indicated by alphabetical code “a; e; l”. In particular, in complex shapes, there are more than one length identified through different alphanumerical codes "a1; a2; a3; l1; l2; l3; l4". | Double | In phytoplankton data template, this field must contain the measured value according to the Atlas of Shapes (https://www.phytovre.lifewatchitaly.eu/vre/shapes-groups/). |
l3 | A 1-D extent quality which is equal to the distance between two points expressed in micrometer and indicated by alphabetical code “a; e; l”. In particular, in complex shapes, there are more than one length identified through different alphanumerical codes "a1; a2; a3; l1; l2; l3; l4". | Double | In phytoplankton data template, this field must contain the measured value according to the Atlas of Shapes (https://www.phytovre.lifewatchitaly.eu/vre/shapes-groups/). | |
l4 | A 1-D extent quality which is equal to the distance between two points expressed in micrometer and indicated by alphabetical code “a; e; l”. In particular, in complex shapes, there are more than one length identified through different alphanumerical codes "a1; a2; a3; l1; l2; l3; l4". | Double | In phytoplankton data template, this field must contain the measured value according to the Atlas of Shapes (https://www.phytovre.lifewatchitaly.eu/vre/shapes-groups/). | |
d11 | A 1-D extent quality which is equal to the distance from one side of an object to another side which is opposite, expressed in micrometer and i ndicated by alphabetical code “b; d ”. In particular, in complex shapes, there are more than one width identified through different alphanumerical codes "b1; b2; b3; b4; d1; d11; d2; d22; d3; d33; d4; d44". | Double | In phytoplankton data template, this field must contain the measured value according to the Atlas of Shapes (https://www.phytovre.lifewatchitaly.eu/vre/shapes-groups/). | |
d22 | A 1-D extent quality which is equal to the distance from one side of an object to another side which is opposite, expressed in micrometer and i ndicated by alphabetical code “b; d ”. In particular, in complex shapes, there are more than one width identified through different alphanumerical codes "b1; b2; b3; b4; d1; d11; d2; d22; d3; d33; d4; d44". | Double | In phytoplankton data template, this field must contain the measured value according to the Atlas of Shapes (https://www.phytovre.lifewatchitaly.eu/vre/shapes-groups/). | |
d33 | A 1-D extent quality which is equal to the distance from one side of an object to another side which is opposite, expressed in micrometer and i ndicated by alphabetical code “b; d ”. In particular, in complex shapes, there are more than one width identified through different alphanumerical codes "b1; b2; b3; b4; d1; d11; d2; d22; d3; d33; d4; d44". | Double | In phytoplankton data template, this field must contain the measured value according to the Atlas of Shapes (https://www.phytovre.lifewatchitaly.eu/vre/shapes-groups/). | |
d44 | A 1-D extent quality which is equal to the distance from one side of an object to another side which is opposite, expressed in micrometer and i ndicated by alphabetical code “b; d ”. In particular, in complex shapes, there are more than one width identified through different alphanumerical codes "b1; b2; b3; b4; d1; d11; d2; d22; d3; d33; d4; d44". | Double | In phytoplankton data template, this field must contain the measured value according to the Atlas of Shapes (https://www.phytovre.lifewatchitaly.eu/vre/shapes-groups/). | |
biovolume | Total volume of a single cell or colony expressed in cubic micrometers. It is calculated according to the geometric equations, after association of geometric shape to the real shape of the organism and measurements of linear dimensions (e.g., length, width,) for each single cell or colony. | Double | ||
cellcarboncontent | Cellular carbon content of phytoplankton organisms expressed in picograms and determined directly as particulate organic carbon or obtained indirectly by converting cell biovolume into carbon using empirically or theoretically derived equations. | Double | ||
density | The total number of organisms per unit volume of the water sample expressed in liter. This can be individual density or the density calculated at higher level (species/taxon) if the dataset is structured at community level. | NA | Double | |
totalbiovolume | The total volume is the individual volume of the organism multiplied by its density (cubic micrometer per liter). This can be calculated at higher level (species/taxon) if the dataset is structured at community level. | NA | Double | |
totalcarboncontent | The total carbon content is the carbon content of the organism multiplied by density (picogram per liter). This can be calculated at higher level (species/taxon) if the dataset is structured at community level. | NA | Double |