suggest to support EML json to define table structures

[jhpoelen]

Following example by @zedomel in globalbioticinteractions/carvalheiro2023@23d3ba6#diff-8e200691cc9a15b8059aab1f16475a480536b1b07858c89e58aedcd126d44215

[jhpoelen]

@mbjones - an EML question - is there a preferred filename for a eml metadata descriptor for a dataset?

eml.json
eml.xml
metadata.xml
metadata.json

What do you typically encounter when working with DataONE datasets?

[mbjones]

For EML, we see everything under the sun, but mostly people use the .xml extension. For the name, we see either a project-based name like some-project-2006.xml, and less frequently we'll see a generic name like metadata.xml. For our own data packages, we name the metadata files from the dataset title, mangled to remove illegal and non-printing characters from the filename. For example, for the DOI https://doi.org/10.18739/A2ZS2KF4B we have the metadata filename Retrogressive_thaw_slump_data_derived_from_ArcticD.xml.

[jhpoelen]

@mbjones thanks for sharing your insights on use/naming of of eml files.

[jhpoelen]

A first pass at using EML to define table schemas for species interaction data tables is available via

elton v0.12.13

@zedomel @Filipi-Soares

example:

elton pull globalbioticinteractions/carvalheiro2023

yields

updating [globalbioticinteractions/carvalheiro2023]... done.

followed by

elton interactions globalbioticinteractions/carvalheiro2023\
  | head -n2\
  | mlr --itsvlite --oxtab cat

yields:

argumentTypeId                         https://en.wiktionary.org/wiki/support
sourceOccurrenceId                     
sourceCatalogNumber                    
sourceCollectionCode                   
sourceCollectionId                     
sourceInstitutionCode                  
sourceTaxonId                          
sourceTaxonName                        Pilosella oficinarum
sourceTaxonRank                        species
sourceTaxonPathIds                     
sourceTaxonPath                        Plantae
sourceTaxonPathNames                   kingdom
sourceBodyPartId                       
sourceBodyPartName                     
sourceLifeStageId                      
sourceLifeStageName                    
sourceSexId                            
sourceSexName                          
interactionTypeId                      http://purl.obolibrary.org/obo/RO_0002623
interactionTypeName                    flowersVisitedBy
targetOccurrenceId                     
targetCatalogNumber                    
targetCollectionCode                   
targetCollectionId                     
targetInstitutionCode                  
targetTaxonId                          
targetTaxonName                        Andrena
targetTaxonRank                        genus
targetTaxonPathIds                     
targetTaxonPath                        Hymenoptera | Andrenidae
targetTaxonPathNames                   order | family
targetBodyPartId                       
targetBodyPartName                     
targetLifeStageId                      
targetLifeStageName                    
targetSexId                            
targetSexName                          
basisOfRecordId                        
basisOfRecordName                      
http://rs.tdwg.org/dwc/terms/eventDate 
decimalLatitude                        
decimalLongitude                       
localityId                             
localityName                           England
referenceDoi                           
referenceUrl                           https://docs.google.com/spreadsheets/u/1/d/1cJ0qX9ppqHoSyqFykwYJef-DFOzoutthBXjwKRY81T8/export?format=tsv&id=1cJ0qX9ppqHoSyqFykwYJef-DFOzoutthBXjwKRY81T8&gid=776329546
referenceCitation                      https://docs.google.com/spreadsheets/u/1/d/1cJ0qX9ppqHoSyqFykwYJef-DFOzoutthBXjwKRY81T8/export?format=tsv&id=1cJ0qX9ppqHoSyqFykwYJef-DFOzoutthBXjwKRY81T8&gid=776329546
namespace                              globalbioticinteractions/carvalheiro2023
citation                               WorldFAIR pilot data from: VisitationData_Luisa_Carvalheiro.
archiveURI                             https://github.com/globalbioticinteractions/carvalheiro2023/archive/f498352c233d0172af29df964406f170c072d668.zip
lastSeenAt                             2023-11-28T21:44:11.747Z
contentHash                            8c8dea35d77ca7e73702839e3753a147215fdfd70886974ff434a24330247597
eltonVersion                           0.12.13

[jhpoelen]

feature is working as expected, @zedomel et al. please holler if you find any issues or have any suggestions.