Accepted values in EML package vs ecoinformatics schema description

[BenMerSci]

I'm sorry in advance if this is silly and obvious, but I can't seem to find a clear answer anywhere.

I'm currently trying to build a dummy EML for testing, and I'm using the schema documentation from https://eml.ecoinformatics.org/schema/ to understand the different possible tags and values for each field.

I was trying to recreate a small EML with the creator, contact, pubDate, abstract, and intellectualRights fields. I'm working with a lot of GBIF data, so I wanted to mimic how they populate their intellectualRights field, which seems to be inline with what is documented at https://eml.ecoinformatics.org/schema/:

intellectualRights has three sub-tags: section, para and markdown, and I think GBIF uses it mostly like so:

intellectual_rights <- list( para = list( #text= "This work is licensed under a.", ulink = list(@url = "http://creativecommons.org/licenses/by/4.0/legalcode", citetitle = "Creative Commons Attribution (CC-BY) 4.0 License" ) ) )

which doesn't seem to be supported by the package EML as eml_validate() returns errors however I try to twist it with these different tags. I've seen that in the package documentation the intellectualRights field is provided as a plain string.

I'm trying to understand the difference between the documentation of the dataset schema from ecoinformatics, and what is accepted (validates) from the EML package.

Thank you!

[mbjones]

@BenMerSci you should see the same results from the EML schema validator and the EML R package, as the R package rules are derived from the schema. If you post the errors you are seeing, then it would be easier to help interpret what is going on in terms of validation. It's probably some minor syntax or encoding issue. Can you post a little reproducible script that generates the error?

In this particular case, I'll note that the GBIF pattern is a but outdated, as EML 2.2.0 introduced new fields specifically for structured license URLs. You can use these in addition to the textual statement in intellectualRights, so it is not either/or. See https://eml.ecoinformatics.org/whats-new-in-eml-2-2-0#dataset-license. In general, it is better to provide license URLs and information in the licensed tag than it is in intellectualRights.

[mbjones]

I'm not sure what code you are running per se, but here's a simple snippet that creates a valid EML document with an intellectualRights statement with a link, and a licensed field with the license URL. Hope its helpful.

library(EML)
library(emld)
library(uuid)

me <- as_emld(person("Matt", "Jones", ,"me@example.com", "cre"))

intellectual_rights <- list(markdown=set_TextType(text="This work is licensed under a [Creative Commons Attribution (CC-BY) 4.0 License](http://creativecommons.org/licenses/by/4.0/legalcode)."))

licensed <- list(licenseName='Creative Commons Attribution (CC-BY) 4.0 License',
                 url='http://creativecommons.org/licenses/by/4.0/legalcode')

dataset <- list(
               title = 'Test dataset',
               creator = me,
               intellectualRights = intellectual_rights,
               licensed = licensed,
               abstract = 'Simple abstract',
               contact = me)
eml <- list(
           packageId = uuid::UUIDgenerate(),
           system = "uuid", # type of identifier
           dataset = dataset)

write_eml(eml, "/tmp/eml.xml")

eml_validate("/tmp/eml.xml")

[1] TRUE
attr(,"errors")
character(0)

This produces the following EML:

<?xml version="1.0" encoding="UTF-8"?>
<eml:eml xmlns:eml="https://eml.ecoinformatics.org/eml-2.2.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:stmml="http://www.xml-cml.org/schema/stmml-1.2" packageId="fc1175cf-4723-4aa2-9bf8-0e53d4edaf45" system="uuid" xsi:schemaLocation="https://eml.ecoinformatics.org/eml-2.2.0 https://eml.ecoinformatics.org/eml-2.2.0/eml.xsd">
  <dataset>
    <title>Test dataset</title>
    <creator>
      <individualName>
        <givenName>Matt</givenName>
        <surName>Jones</surName>
      </individualName>
      <electronicMailAddress>me@example.com</electronicMailAddress>
    </creator>
    <abstract>Simple abstract</abstract>
    <intellectualRights>
      <markdown>This work is licensed under a [Creative Commons Attribution (CC-BY) 4.0 License](http://creativecommons.org/licenses/by/4.0/legalcode).</markdown>
    </intellectualRights>
    <licensed>
      <licenseName>Creative Commons Attribution (CC-BY) 4.0 License</licenseName>
      <url>http://creativecommons.org/licenses/by/4.0/legalcode</url>
    </licensed>
    <contact>
      <individualName>
        <givenName>Matt</givenName>
        <surName>Jones</surName>
      </individualName>
      <electronicMailAddress>me@example.com</electronicMailAddress>
    </contact>
  </dataset>
</eml:eml>

[BenMerSci]

Here is a little example that fails on my side for the intellectualRights field:

title <- "Test title"

creator <- EML::set_responsibleParty(
  givenName = "Benjamin",
  surName = "Mercier",
  organizationName = "Test organization",
  electronicMailAddress = "test@test.com"
)

contact <- EML::set_responsibleParty(
  givenName = "Benjamin",
  surName = "Mercier",
  organizationName = "Test organization",
  electronicMailAddress = "test@test.com"
)

intellectual_rights <- list(
  para = list(
    "This work is licensed under a.",
    ulink = list(
      `@url` = "http://creativecommons.org/licenses/by/4.0/legalcode",
      citetitle = "Creative Commons Attribution (CC-BY) 4.0 License"
    )
  )
)

eml <- list(
  packageId = uuid::UUIDgenerate(),
  system = "uuid",
  dataset = list(
    title = title,
    creator = creator,
    contact = contact,
    intellectualRights = intellectual_rights
  )
)

EML::eml_validate(eml)

returns the error:
Error in if (grepl("<\\w+>", x[[i]])) { : the condition has length > 1

Its probably a syntax error of how I define the sub-tags within the list().

I also had a problem with the distribution field, but it worked with this snippet:

distribution <- list(
  online = list(
    url = list(
      `function` = "information",
      "https://test.com/info"
    )
  )
)

And perfect for the licensed field, I will absolutely use this instead of intellectualRights for providing information about the license! I guess my problem with the intellectualRights field doesn't really matter anymore, especially with the GBIF format using the para tag, with ulink, since I can use the licensed tag and if I need the intellectualRights field I can use it like you suggested with the markdown tag!

I guess this was never an issue and we can close this. I'm a bit new with EML and wasn't aware that it was preferred to use the licensed tag. This was a bit of wasted time, I'm sorry!

Thank you @mbjones !