add support for linking names to Plazi-enabled taxonomic literature.

[jhpoelen]

https://plazi.org make taxonomic literature machine readable and link taxonomic names to their taxonomic treatments. One of the ways Plazi share these links is through GBIF (e.g., https://www.gbif.org/dataset/6384b520-7e9f-4874-a414-76c2e9b01d74 for Horseshoe bats).

Suggest to add support for Nomer to easily link a taxonomic name to it's plazi treatment.

For instance, when running:

$ echo -e "\tRhinolophus denti Thomas 1904" | nomer append plazi-names

an expected result would be

provided id	provided name	resolved id	resolved name
	Rhinolophus denti Thomas 1904	http://treatment.plazi.org/id/885887A2FFC88A21F8B1FA48FB92DD65	Rhinolophus denti

Ideally, globalnames would enable this kind of linkages (see GlobalNamesArchitecture/dwca_hunter#30), but alternatives are possible also (e.g., index dwc-a via plazi ipt or similar).

fyi @myrmoteras @dimus

[jhpoelen]

Using wikidata to search for Plazi treatments:

$ echo -e "WORMS:126436\tGadus morhua" | nomer append wikidata-taxon-id-web
using matcher [wikidata-taxon-id-web]
WORMS:126436	Gadus morhua	SAME_AS	WD:Q199788	Gadus morhua			Gadus morhua			https://www.wikidata.org/wiki/Q199788	
WORMS:126436	Gadus morhua	SAME_AS	NCBI:8049	Gadus morhua			Gadus morhua			https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=8049	
WORMS:126436	Gadus morhua	SAME_AS	ITIS:164712	Gadus morhua			Gadus morhua			http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=164712	
WORMS:126436	Gadus morhua	SAME_AS	GBIF:2415835	Gadus morhua			Gadus morhua			http://www.gbif.org/species/2415835	
WORMS:126436	Gadus morhua	SAME_AS	WORMS:126436	Gadus morhua			Gadus morhua			https://www.marinespecies.org/aphia.php?p=taxdetails&id=126436	
WORMS:126436	Gadus morhua	SAME_AS	FBC:FB:SpecCode:69	Gadus morhua			Gadus morhua			http://fishbase.org/summary/69	
WORMS:126436	Gadus morhua	SAME_AS	PLAZI:99915444-EC70-3196-7F2D-637F418F0730	Gadus morhua			Gadus morhua		http://treatment.plazi.org/id/99915444-EC70-3196-7F2D-637F418F0730	
WORMS:126436	Gadus morhua	SAME_AS	INAT_TAXON:63740	Gadus morhua			Gadus morhua			https://inaturalist.org/taxa/63740	
WORMS:126436	Gadus morhua	SAME_AS	NBN:NBNSYS0000175392	Gadus morhua			Gadus morhua			https://data.nbn.org.uk/Taxa/NBNSYS0000175392	
WORMS:126436	Gadus morhua	SAME_AS	IRMNG:11195684	Gadus morhua			Gadus morhua			http://www.marine.csiro.au/mirrorsearch/ir_search.list_species?sp_id=11195684	

Note however, that, for some reason, the treatment for Gadus morhua does not seem to resolve on the Plazi server (see attached screenshot)

http://treatment.plazi.org/id/99915444-EC70-3196-7F2D-637F418F0730

[jhpoelen]

@myrmoteras @mguidoti any idea why http://treatment.plazi.org/id/99915444-EC70-3196-7F2D-637F418F0730 , a treatment provided for Gadus morhua by wikidata / wikipedia does not resolve on the Plazi servers?

[jhpoelen]

@myrmoteras suggested to use Synospecies instead via https://synospecies.plazi.org/advanced or https://synospecies.plazi.org/ . The wikidata linked information is said to be incomplete and out of date.

[jhpoelen]

Very neat to see that Plazi publishes their >300k treatment meta-data as versioned and structured data via https://github.com/plazi/treatments-rdf/, enabling bulk data integration via tools like Nomer. Thank you Plazi!

[jhpoelen]

A plazi matcher was implemented. The following result was produced:

echo -e "\tRhinolophus sinicus" | nomer append plazi
	Rhinolophus sinicus	SAME_AS	http://treatment.plazi.org/id/885887A2FFE18A06F899F4EFF9BFD35B	Rhinolophus sinicus	speciesAnimalia | Chordata | Mammalia | Chiroptera | Rhinolophidae | Rhinolophus | Rhinolophus sinicus		kingdom | phylum | class | order | family | genus | species	http://treatment.plazi.org/id/885887A2FFE18A06F899F4EFF9BFD35B

[jhpoelen]

After some more modifications, all related treatments are linked, including the doi of the original publications:

--	provided name	link type	linked id	linked taxon name	...	...	...	...	...	...
...	Rhinolophus sinicus	SAME_AS	http://treatment.plazi.org/id/885887A2FFE18A06F899F4EFF9BFD35B	Rhinolophus sinicus			Animalia | Chordata | Mammalia | Chiroptera | Rhinolophidae | Rhinolophus | Rhinolophus sinicus		kingdom | phylum | class | order | family | genus | species	http://treatment.plazi.org/id/885887A2FFE18A06F899F4EFF9BFD35B
	Rhinolophus sinicus	SAME_AS	doi:10.5281/zenodo.3808964	Rhinolophus sinicus			Animalia | Chordata | Mammalia | Chiroptera | Rhinolophidae | Rhinolophus | Rhinolophus sinicus		kingdom | phylum | class | order | family | genus | species	https://doi.org/10.5281/zenodo.3808964
	Rhinolophus sinicus	SAME_AS	http://treatment.plazi.org/id/03AF87D3C435B542FF728049FB55BB1B	Rhinolophus sinicus			Animalia | Chordata | Mammalia | Chiroptera | Rhinolophidae | Rhinolophus | Rhinolophus sinicus		kingdom | phylum | class | order | family | genus | species	http://treatment.plazi.org/id/03AF87D3C435B542FF728049FB55BB1B
	Rhinolophus sinicus	SAME_AS	doi:10.3161/150811009X465703	Rhinolophus sinicus			Animalia | Chordata | Mammalia | Chiroptera | Rhinolophidae | Rhinolophus | Rhinolophus sinicus		kingdom | phylum | class | order | family | genus | species	https://doi.org/10.3161/150811009X465703
	Rhinolophus sinicus	SAME_AS	http://treatment.plazi.org/id/03D7CF296C71FF8C2C88F6BDF85AF415	Rhinolophus sinicus			Animalia | Chordata | Mammalia | Chiroptera | Rhinolophidae | Rhinolophus | Rhinolophus sinicus		kingdom | phylum | class | order | family | genus | species	http://treatment.plazi.org/id/03D7CF296C71FF8C2C88F6BDF85AF415
	Rhinolophus sinicus	SAME_AS	doi:10.5281/zenodo.3805455	Rhinolophus sinicus			Animalia | Chordata | Mammalia | Chiroptera | Rhinolophidae | Rhinolophus | Rhinolophus sinicus		kingdom | phylum | class | order | family | genus | species	https://doi.org/10.5281/zenodo.3805455

More feature can be imagined (e.g., synonyms, more name link types), but a first pass has been implemented.

[myrmoteras]

Super. I link this with the T.rex project to make sure the data flow works

[jhpoelen]

Here's an example a search with some Plazi-enabled links obtained via https://www.globalbioticinteractions.org/?sourceTaxon=Coronaviridae . Note the DOI and Plazi labels point to links:

http://taxon-concept.plazi.org/id/Animalia/Scotophilus_kuhlii_Leach_1821

https://doi.org/10.3161/150811013X667993

http://treatment.plazi.org/id/690487A5FFE7FFAA0C25F8EDFCAAD7BC

[jhpoelen]

This newly added feature was used to implement methods and produce results:

Methods

The automated taxon link procedure is described in Poelen, Jorrit H. (2020). Global Biotic Interactions: Taxon Graph Patches (Version 0.5) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.4062711 .

Result

The automated patch procedure was applied to GloBI Taxon Graph v0.3.25 to produce:Poelen, Jorrit H. (2020). Global Biotic Interactions: Taxon Graph (Version 0.3.26) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.4062765 - 41,894 Plazi treatments were linked, covering 27,721 Plazi taxon concepts and 9,346 original publications.