search

ropensci / taxa

taxonomic classes for R
https://docs.ropensci.org/taxa
Other
48 stars 12 forks source link

implement mapping to/support for darwin core terms #101

Open sckott opened 6 years ago

sckott commented 6 years ago

http://rs.tdwg.org/dwc/terms/#Taxon

Not sure yet where the best place is to put this support.

May want to not mess with the current functions, that is, allow users that don't want to deal with dwc to not worry about it, but for people that do care we can provide lower level interface or additional parameters to specify things wrt dwc

Some things can likely be automatically mapped to dwc taxonomy terms, but some others perhaps not

sckott commented 6 years ago

Features:

sckott commented 6 years ago

current feeling is that we may want to implement a sister pkg for dwc serialization support, but will have a play and see how it goes

zachary-foster commented 6 years ago

I dont think I understand this issue. Can you give me some background? Thx!

sckott commented 6 years ago

So Darwin Core is a standard for data and metadata around biodiversity data, and it includes taxonomy

http://rs.tdwg.org/dwc/terms/index.htm#taxonindex includes lots of terms

taxonID | scientificNameID | acceptedNameUsageID | parentNameUsageID | originalNameUsageID | nameAccordingToID | namePublishedInID | taxonConceptID | scientificName | acceptedNameUsage | parentNameUsage | originalNameUsage | nameAccordingTo | namePublishedIn | namePublishedInYear | higherClassification | kingdom | phylum | class | order | family | genus | subgenus | specificEpithet | infraspecificEpithet | taxonRank | verbatimTaxonRank | scientificNameAuthorship | vernacularName | nomenclaturalCode | taxonomicStatus | nomenclaturalStatus | taxonRemarks

and theres data formats too, XML based, theres some egs here https://github.com/ropensci/finch/tree/master/inst/examples

I think the main use case would be to map our objects in this pkg to what Darwin Core expects, and serialize to XML (and possibly read from into taxa classes) so that users can create (or edit and re-save to disk) darwin core

it may make sense to do a separate package, haven't explored yet

zachary-foster commented 6 years ago

Sounds cool, thanks!

sckott commented 6 years ago

the only question i got on my talk about taxonomy in R at TDWG in ottawa last fall was about whether we'd considered darwin core

zachary-foster commented 6 years ago

Seems like a good application of taxa, particularly taxmap. I am working on similar pairs of parsers and writers for formats used in microbiome research in metacoder, so people can read, edit, save. But yea, probably best in another package since it is for a specific format

sckott commented 6 years ago

will see if fits in finch first