Transforms the metadata of a published Movebank dataset (with a DOI) to an Ecological Metadata Language (EML) file.
Arguments
- doi
DOI of the original dataset, used to get metadata.
- directory
Path to local directory to write files to.
- contact
Person to be set as resource contact and metadata provider. To be provided as a
person().- study_id
Identifier of the Movebank study from which the dataset was derived (e.g.
1605797471for this study).- derived_paragraph
If
TRUE, a paragraph will be added to the abstract, indicating that data have been transformed usingwrite_dwc().
Value
eml.xml file written to disk.
And invisibly, an EML::eml object.
Details
The resulting EML file can be uploaded to an IPT
for publication to GBIF and/or OBIS.
A corresponding Darwin Core Archive can be created with write_dwc().
See vignette("movepub") for an example.
Transformation details
Metadata are derived from the original dataset by looking up its doi in
DataCite (example)
and transforming these to EML.
The following properties are set:
title: Original dataset title.
description: Original dataset description. If
derived_paragraph = TRUEa generated paragraph is added, e.g.:Data have been standardized to Darwin Core using the movepub R package and are downsampled to the first GPS position per hour. The original data are available in Dijkstra et al. (2023, https://doi.org/10.5281/zenodo.10053903), a deposit of Movebank study 1605797471.
license: License of the original dataset.
creators: Creators of the original dataset.
contact:
contactor first creator of the original dataset.metadata provider:
contactor first creator of the original dataset.keywords: Keywords of the original dataset.
alternative identifier: DOI of the original dataset. As a result, no new DOI will be created when publishing to GBIF.
external link and alternative identifier: URL created from
study_idor the firstderived fromrelated identifier in the original dataset.
The following properties are not set:
type
subtype
update frequency
publishing organization
geographic coverage
taxonomic coverage
temporal coverage
associated parties
project data
sampling methods
citations
collection data: not applicable.
See also
Other dwc functions:
write_dwc()
Examples
(write_eml(doi = "10.5281/zenodo.10053903", directory = "my_directory"))
#>
#> ── Writing file ──
#>
#> • my_directory/eml.xml
#> $packageId
#> [1] "be18c011-e382-40b1-a0fe-1dbc92dc8e0d"
#>
#> $system
#> [1] "uuid"
#>
#> $dataset
#> $dataset$title
#> [1] "O_ASSEN - Eurasian oystercatchers (Haematopus ostralegus, Haematopodidae) breeding in Assen (the Netherlands)"
#>
#> $dataset$abstract
#> $dataset$abstract$para
#> [1] "O_ASSEN - Eurasian oystercatchers (Haematopus ostralegus, Haematopodidae) breeding in Assen (the Netherlands) is a bird tracking dataset published by the Vogelwerkgroep Assen, Netherlands Institute of Ecology (NIOO-KNAW), Sovon, Radboud University, the University of Amsterdam and the Research Institute for Nature and Forest (INBO). It contains animal tracking data collected for the study O_ASSEN using trackers developed by the University of Amsterdam Bird Tracking System (UvA-BiTS, http://www.uva-bits.nl). The study was operational from 2018 to 2019. In total 6 individuals of Eurasian oystercatchers (Haematopus ostralegus) have been tagged as a breeding bird in the city of Assen (the Netherlands), mainly to study space use of oystercatchers breeding in urban areas. Data are uploaded from the UvA-BiTS database to Movebank and from there archived on Zenodo (see https://github.com/inbo/bird-tracking). No new data are expected.\n\nSee van der Kolk et al. (2022, https://doi.org/10.3897/zookeys.1123.90623) for a more detailed description of this dataset.\n\nFiles\n\nData in this package are exported from Movebank study 1605797471. Fields in the data follow the Movebank Attribute Dictionary and are described in datapackage.json. Files are structured as a Frictionless Data Package. You can access all data in R via https://zenodo.org/records/10053903/files/datapackage.json using frictionless.\n\n\n\ndatapackage.json: technical description of the data files.\n\nO_ASSEN-reference-data.csv: reference data about the animals, tags and deployments.\n\nO_ASSEN-gps-yyyy.csv.gz: GPS data recorded by the tags, grouped by year.\n\nO_ASSEN-acceleration-yyyy.csv.gz: acceleration data recorded by the tags, grouped by year.\n\n\nAcknowledgements\n\nThese data were collected by Bert Dijkstra and Rinus Dillerop from Vogelwerkgroep Assen, in collaboration with the Netherlands Institute of Ecology (NIOO-KNAW), Sovon, Radboud University and the University of Amsterdam (UvA). Funding was provided by the Prins Bernard Cultuurfonds Drenthe, municipality of Assen, IJsvogelfonds (from Birdlife Netherlands and Nationale Postcodeloterij) and the Waterleiding Maatschappij Drenthe. The dataset was published with funding from Stichting NLBIF - Netherlands Biodiversity Information Facility."
#> [2] "This version adds alt-project-id to the reference-data and references the latest Movebank Attribute Dictionary."
#> [3] "<![CDATA[<span></span>Data have been standardized to Darwin Core using the <a href=\"https://inbo.github.io/movepub/\">movepub</a> R package and are downsampled to the first GPS position per hour. The original data are available in Dijkstra et al. (2023, <a href=\"https://doi.org/10.5281/zenodo.10053903\">https://doi.org/10.5281/zenodo.10053903</a>), a deposit of Movebank study <a href=\"https://www.movebank.org/cms/webapp?gwt_fragment=page=studies,path=study1605797471\">1605797471</a>.]]>"
#>
#>
#> $dataset$keywordSet
#> $dataset$keywordSet[[1]]
#> $dataset$keywordSet[[1]]$keywordThesaurus
#> [1] "n/a"
#>
#> $dataset$keywordSet[[1]]$keyword
#> [1] "animal movement" "animal tracking" "gps tracking" "accelerometer"
#> [5] "altitude" "temperature" "biologging" "birds"
#> [9] "UvA-BiTS" "Movebank" "frictionlessdata"
#>
#>
#>
#> $dataset$creator
#> $dataset$creator[[1]]
#> '@id': ~
#> address: ~
#> electronicMailAddress: ~
#> individualName:
#> givenName: Bert
#> surName: Dijkstra
#> onlineUrl: ~
#> organizationName: ~
#> phone: ~
#> positionName: ~
#> userId: ~
#>
#> $dataset$creator[[2]]
#> '@id': ~
#> address: ~
#> electronicMailAddress: ~
#> individualName:
#> givenName: Rinus
#> surName: Dillerop
#> onlineUrl: ~
#> organizationName: ~
#> phone: ~
#> positionName: ~
#> userId: ~
#>
#> $dataset$creator[[3]]
#> '@id': ~
#> address: ~
#> electronicMailAddress: ~
#> individualName:
#> givenName: Kees
#> surName: Oosterbeek
#> onlineUrl: ~
#> organizationName: ~
#> phone: ~
#> positionName: ~
#> userId: ~
#>
#> $dataset$creator[[4]]
#> '@id': ~
#> address: ~
#> electronicMailAddress: ~
#> individualName:
#> givenName: Willem
#> surName: Bouten
#> onlineUrl: ~
#> organizationName: ~
#> phone: ~
#> positionName: ~
#> userId:
#> directory: https://orcid.org/
#> '': 0000-0002-5250-8872
#>
#> $dataset$creator[[5]]
#> '@id': ~
#> address: ~
#> electronicMailAddress: ~
#> individualName:
#> givenName: Peter
#> surName: Desmet
#> onlineUrl: ~
#> organizationName: ~
#> phone: ~
#> positionName: ~
#> userId:
#> directory: https://orcid.org/
#> '': 0000-0002-8442-8025
#>
#> $dataset$creator[[6]]
#> '@id': ~
#> address: ~
#> electronicMailAddress: ~
#> individualName:
#> givenName: Henk-Jan
#> surName: van der Kolk
#> onlineUrl: ~
#> organizationName: ~
#> phone: ~
#> positionName: ~
#> userId:
#> directory: https://orcid.org/
#> '': 0000-0002-8023-379X
#>
#> $dataset$creator[[7]]
#> '@id': ~
#> address: ~
#> electronicMailAddress: ~
#> individualName:
#> givenName: Bruno J.
#> surName: Ens
#> onlineUrl: ~
#> organizationName: ~
#> phone: ~
#> positionName: ~
#> userId:
#> directory: https://orcid.org/
#> '': 0000-0002-4659-4807
#>
#>
#> $dataset$contact
#> '@id': ~
#> address: ~
#> electronicMailAddress: ~
#> individualName:
#> givenName: Bert
#> surName: Dijkstra
#> onlineUrl: ~
#> organizationName: ~
#> phone: ~
#> positionName: ~
#> userId: ~
#>
#> $dataset$pubDate
#> [1] "2023-10-30"
#>
#> $dataset$alternateIdentifier
#> [1] "https://doi.org/10.5281/zenodo.10053903"
#> [2] "https://www.movebank.org/cms/webapp?gwt_fragment=page=studies,path=study1605797471"
#>
#> $dataset$intellectualRights
#> $dataset$intellectualRights$para
#> [1] "cc0-1.0"
#>
#>
#> $dataset$metadataProvider
#> '@id': ~
#> address: ~
#> electronicMailAddress: ~
#> individualName:
#> givenName: Bert
#> surName: Dijkstra
#> onlineUrl: ~
#> organizationName: ~
#> phone: ~
#> positionName: ~
#> userId: ~
#>
#> $dataset$distribution
#> $dataset$distribution$scope
#> [1] "document"
#>
#> $dataset$distribution$online
#> $dataset$distribution$online$url
#> $dataset$distribution$online$url$`function`
#> [1] "information"
#>
#> $dataset$distribution$online$url[[2]]
#> [1] "https://www.movebank.org/cms/webapp?gwt_fragment=page=studies,path=study1605797471"
#>
#>
#>
#>
#>
# Clean up (don't do this if you want to keep your files)
unlink("my_directory", recursive = TRUE)