In lifewatch/lwdataexplorer: Access to data from the LifeWatch Data Explorer
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
warning = FALSE,
message = FALSE
)
Traits data from the World Register of Marine Species (WoRMS).
- Partners: Marine Species Traits editorial board, Flanders Marine Institute (VLIZ), EMODnet Biology, LifeWatch Species Information Backbone
- Period: Taxonomy since 1758 (Linnaeus) and traits data collection since 2014 (start EMODnet Biology pilot projects)
- Geographical coverage: World
- Taxonomic coverage: Biota
- Moratorium: None
- Data quality: Research-grade
How to interpret this dataset
Query options
- Taxon: Select the taxon you are interested in. You can only select one taxon at a time. If the taxon does not appear in the picklist, then it means we don’t have any traits available for that taxon.
- Include traits from child taxa: Check this box if you want to return all children within a certain taxon.
- Traits: You can select a single trait or a combination of traits for a specific taxon.
- Include: If you select two (or more) traits (e.g. macrobenthos and mobile), then the explorer will look for the taxa that are either macrobenthos or mobile (“ANY of selected traits”). If you want to look for taxa that have both traits, then check “ALL of selected traits”.
- Restrict to life stage: You can restrict your search to a specific life stage (e.g. adult, larvae).
- Restrict to species found in these regions: You can combine the selected traits with standardized distributions based on distributions from literature in WoRMS and occurrences in OBIS. This way you can create a list of species which occur in a certain area and which have a certain trait (e.g. all meiobenthos Nematoda species in the North Sea). The explorer is not able to give a list of all species within a certain area. Always use the standardized distributions filter in combination with the traits filter.
- Output: Every parameter is shown in a separate column in the data table. Select “Add classification” if you want to include the higher taxonomic classification to your results. “Compact traits in one row” is unchecked by default. If you check this box, the sourceID column is dropped and same values in one column are taken together where possible. Checking this box slows down the querying process however.
Available columns
- Aphiaid: Unique identifier for a taxon in WoRMS.
- Scientificname: Scientific name of the taxon.
- Scientificnameauthorship: Scientific authority of the taxon.
- Taxonomicstatus: Taxonomic status of the taxon. For the available statuses we refer to Horton et al., 2017 (https://marinespecies.org/aphia.php?p=manual)
Click to see all the columns available:
- Taxonrankid: Database ID of the rank of the taxon in WoRMS (e.g. 220 is species, 180 is genus).
- Highertaxonid: AphiaID of the higher taxon in WoRMS.
- Acceptednameusageid: AphiaID of the accepted name of the taxon in WoRMS.
- Acceptednameusage: Accepted name of the taxon in WoRMS.
- Kingdom: Kingdom of the taxon in WoRMS.
- Phylum: Phylum of the taxon in WoRMS.
- Class: Class of the taxon in WoRMS.
- Order: Order of the taxon in WoRMS.
- Family: Family of the taxon in WoRMS.
- Genus: Genus of the taxon in WoRMS.
- Ismarine: Marine environment flag of the taxon in WoRMS. 1 = marine, 0 = not marine, null = marine flag not filled in.
- Aphiaid_inherited: AphiaID of the higher taxon from which the trait was inherited.
- Sourceid: Database ID of the trait source in WoRMS.
- Qualitystatusid: Database ID of the quality status of the taxon in WoRMS. 2 = Added by Database Management Team, 3 = Checked by Taxonomic Editor, 4 = Edited by Database Management Team, 5 = Added/edited by Thematic Editor.
- Isbrackish: Brackish environment flag of the taxon in WoRMS. 1 = brackish, 0 = not brackish, null = brackish flag not filled in.
- Isfreshwater: Freshwater environment flag of the taxon in WoRMS. 1 = freshwater, 0 = not freshwater, null = freshwater flag not filled in.
- Species: Species name according to WoRMS.
- Isterrestrial: Terrestrial environment flag of the taxon in WoRMS. 1 = terrestrial, 0 = not terrestrial, null = terrestrial flag not filled in.
- Subgenus: Subgenus of the taxon in WoRMS.
- Isextinct: Extinct flag of the taxon in WoRMS. 1 = extinct, 0 = not extinct, null = not filled in.
- Occurrence: Standardized distributions based on the distributions based on literature in Aphia and the occurrences in OBIS.
- Traitobservedin: Distribution based on literature that is linked to a certain trait (e.g. Copepods can have different body sizes in different areas).
- Trait note: Additional information about the trait added as a note with the trait in WoRMS.
- Life stage: Life stage of the taxon. (https://marinespecies.org/traits/aphia.php?p=attrdefinitions)
- AMBI ecological group: AZTI’s Marine Biotic Index ecological group. (https://marinespecies.org/traits/aphia.php?p=attrdefinitions)
- Asexual reproduction: Whether or not an organism reproduces asexually. (https://marinespecies.org/traits/aphia.php?p=attrdefinitions)
- Body shape: The general shape of the body of an organism. (https://marinespecies.org/traits/aphia.php?p=attrdefinitions)
- Body size: A measurement of the size of the organism. (https://marinespecies.org/traits/aphia.php?p=attrdefinitions)
- Body size_valueincentimeter: A measurement of the size of the organism in centimeter. (https://marinespecies.org/traits/aphia.php?p=attrdefinitions)
- Body size_dimension: The dimension of a body size (e.g. length, width, diameter). (https://marinespecies.org/traits/aphia.php?p=attrdefinitions)
- Body size_type: The type of a body size (e.g. minimum, maximum, average). (https://marinespecies.org/traits/aphia.php?p=attrdefinitions)
- Body size_unit: The unit of a body size (e.g. m, cm, mm). (https://marinespecies.org/traits/aphia.php?p=attrdefinitions)
- Body size (qualitative): Trait that describes the size class of an organism. (https://marinespecies.org/traits/aphia.php?p=attrdefinitions)
- Brooding: Whether or not a species is brooding. (https://marinespecies.org/traits/aphia.php?p=attrdefinitions)
- Calcification: Mode of calcification of seaweed. (https://marinespecies.org/traits/aphia.php?p=attrdefinitions)
- Cytomorphology: Trait that describes whether an organism is unicellular or not. (https://marinespecies.org/traits/aphia.php?p=attrdefinitions)
- Dispersion mode: The pattern of distribution of organisms or populations in space. (https://marinespecies.org/traits/aphia.php?p=attrdefinitions)
- Environmental position: Position relative to substratum or fluid medium (air/water). (https://marinespecies.org/traits/aphia.php?p=attrdefinitions)
- Feedingtype: Feeding type of the organism. (https://marinespecies.org/traits/aphia.php?p=attrdefinitions)
- Feedingtype_host/prey: Trait that describes the host or prey of an organism. (https://marinespecies.org/traits/aphia.php?p=attrdefinitions)
- Fossil range: Chronostratigraphic range of an organism. (https://marinespecies.org/traits/aphia.php?p=attrdefinitions)
- Functional group: Whether a organism belongs to the benthos, plankton, nekton. (https://marinespecies.org/traits/aphia.php?p=attrdefinitions)
- Gamete type: Descriptors of the relative size of gametes. (https://marinespecies.org/traits/aphia.php?p=attrdefinitions)
- Gametophyte arrangement: Trait that describes the male and female reproductive structures. (https://marinespecies.org/traits/aphia.php?p=attrdefinitions)
- Generation time: The average duration of a life cycle between birth and reproduction. (https://marinespecies.org/traits/aphia.php?p=attrdefinitions)
- Larval and juvenile development: Description of how the larvae or juveniles develop into adults. (https://marinespecies.org/traits/aphia.php?p=attrdefinitions)
- Life cycle: The type of life cycle an organism has. (https://marinespecies.org/traits/aphia.php?p=attrdefinitions)
- Life span: Longevity; the maximum or mean duration of life of an individual or group. (https://marinespecies.org/traits/aphia.php?p=attrdefinitions)
- Macroalgal blooming: Types of blooming specific for macroalgae species. (https://marinespecies.org/traits/aphia.php?p=attrdefinitions)
- Mobility: The tendency of an organism or population to change its location or distribution with time; vagility. (https://marinespecies.org/traits/aphia.php?p=attrdefinitions)
- Paraphyletic group: A group of taxa derived from a single ancestral taxon, but one which does not contain all the descendants of the most recent common ancestor. (https://marinespecies.org/traits/aphia.php?p=attrdefinitions)
- Plant habit: The characteristic form in which a given species of plant grows. (https://marinespecies.org/traits/aphia.php?p=attrdefinitions)
- Reproductive frequency: Trait that describes the fertility period of an organism. (https://marinespecies.org/traits/aphia.php?p=attrdefinitions)
- Seasonality: Trait that describes the periodicity of an organism related to the seasons. (https://marinespecies.org/traits/aphia.php?p=attrdefinitions)
- Sociability: Trait that describes an organism's behavioural interactions with members of the same species. (https://marinespecies.org/traits/aphia.php?p=attrdefinitions)
- Spawning: The release of gametes or eggs into the water. (https://marinespecies.org/traits/aphia.php?p=attrdefinitions)
- Species importance to society: Traits related to IUCN Red List, OSPAR, HELCOM, CITES, Habitats Directive, Birds Directive. (https://marinespecies.org/traits/aphia.php?p=attrdefinitions)
- Supporting structure & enclosure: Hard framework, internal or external, which supports and protects softer parts of plant, animal or unicellular organism, and to which muscles usually attach in animals, includes skeletons. (https://marinespecies.org/traits/aphia.php?p=attrdefinitions)
- Thallus vertical space used: Trait that describes whether an organism belongs to the canopy, sub-canopy, turf, or is encrusting. (https://marinespecies.org/traits/aphia.php?p=attrdefinitions)
- Tolerance to pollutants: Trait that describes how tolerant to pollutants an organism is. (https://marinespecies.org/traits/aphia.php?p=attrdefinitions)
- Wave exposure: Trait that describes the range of exposure to wave action in which the organism is recorded. (https://marinespecies.org/traits/aphia.php?p=attrdefinitions)
- Zonation: The distribution of organisms in distinctive areas, layers or zones. (https://marinespecies.org/traits/aphia.php?p=attrdefinitions)
Abstract
# Get the abstract and/or description from IMIS and print here
library(jsonlite)
dasid <- fromJSON("https://www.vliz.be/en/imis?module=dataset&dasid=8131&show=json")
abstract <- dasid[["datasetrec"]][["EngAbstract"]]
description <- dasid[["datasetrec"]][["EngDescr"]]
if (is.null(abstract) & is.null(description)){
} else if(is.null(abstract) & !is.null(description)){
out <- description
} else if(!is.null(abstract) & is.null(description)){
out <- abstract
} else if(!is.null(abstract) & !is.null(description)){
out <- paste0(abstract, "</br>", description)
}
cat(out)
How to cite these data
Marine Species Traits editorial board (2023). Marine Species Traits. Accessed at http://www.marinespecies.org/traits on yyyy-mm-dd. https://doi.org/10.14284/580
Availability: CC-BY
lifewatch/lwdataexplorer documentation built on Aug. 24, 2024, 12:35 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
knitr::opts_chunk$set( collapse = TRUE, comment = "#>", warning = FALSE, message = FALSE )
Traits data from the World Register of Marine Species (WoRMS).
- Partners: Marine Species Traits editorial board, Flanders Marine Institute (VLIZ), EMODnet Biology, LifeWatch Species Information Backbone
- Period: Taxonomy since 1758 (Linnaeus) and traits data collection since 2014 (start EMODnet Biology pilot projects)
- Geographical coverage: World
- Taxonomic coverage: Biota
- Moratorium: None
- Data quality: Research-grade
How to interpret this dataset
Query options
- Taxon: Select the taxon you are interested in. You can only select one taxon at a time. If the taxon does not appear in the picklist, then it means we don’t have any traits available for that taxon.
- Include traits from child taxa: Check this box if you want to return all children within a certain taxon.
- Traits: You can select a single trait or a combination of traits for a specific taxon.
- Include: If you select two (or more) traits (e.g. macrobenthos and mobile), then the explorer will look for the taxa that are either macrobenthos or mobile (“ANY of selected traits”). If you want to look for taxa that have both traits, then check “ALL of selected traits”.
- Restrict to life stage: You can restrict your search to a specific life stage (e.g. adult, larvae).
- Restrict to species found in these regions: You can combine the selected traits with standardized distributions based on distributions from literature in WoRMS and occurrences in OBIS. This way you can create a list of species which occur in a certain area and which have a certain trait (e.g. all meiobenthos Nematoda species in the North Sea). The explorer is not able to give a list of all species within a certain area. Always use the standardized distributions filter in combination with the traits filter.
- Output: Every parameter is shown in a separate column in the data table. Select “Add classification” if you want to include the higher taxonomic classification to your results. “Compact traits in one row” is unchecked by default. If you check this box, the sourceID column is dropped and same values in one column are taken together where possible. Checking this box slows down the querying process however.
Available columns
- Aphiaid: Unique identifier for a taxon in WoRMS.
- Scientificname: Scientific name of the taxon.
- Scientificnameauthorship: Scientific authority of the taxon.
- Taxonomicstatus: Taxonomic status of the taxon. For the available statuses we refer to Horton et al., 2017 (https://marinespecies.org/aphia.php?p=manual)
Click to see all the columns available:
Abstract
# Get the abstract and/or description from IMIS and print here library(jsonlite) dasid <- fromJSON("https://www.vliz.be/en/imis?module=dataset&dasid=8131&show=json") abstract <- dasid[["datasetrec"]][["EngAbstract"]] description <- dasid[["datasetrec"]][["EngDescr"]] if (is.null(abstract) & is.null(description)){ } else if(is.null(abstract) & !is.null(description)){ out <- description } else if(!is.null(abstract) & is.null(description)){ out <- abstract } else if(!is.null(abstract) & !is.null(description)){ out <- paste0(abstract, "</br>", description) } cat(out)
How to cite these data
Marine Species Traits editorial board (2023). Marine Species Traits. Accessed at http://www.marinespecies.org/traits on yyyy-mm-dd. https://doi.org/10.14284/580
Availability: CC-BY
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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