Create a name report - Githubissues

seltmann commented 2 years ago

Automatically align the names from a list or dwc-A and align using a catalog (e.g., catalogOfLife).

For example, given this record from MZC:

id	modified	rightsHolder	references	institutionID	datasetID	institutionCode	collectionCode	ownerInstitutionCode	basisOfRecord	informationWithheld	dynamicProperties	occurrenceID	catalogNumber	recordNumber	recordedBy	recordedByID	individualCount	sex	lifeStage	georeferenceVerificationStatus	occurrenceStatus	preparations	disposition	associatedMedia	associatedOccurrences	associatedSequences	associatedTaxa	otherCatalogNumbers	occurrenceRemarks	fieldNumber	eventDate	startDayOfYear	year	month	day	verbatimEventDate	habitat	samplingProtocol	higherGeographyID	higherGeography	continent	waterBody	islandGroup	island	country	countryCode	stateProvince	county	locality	verbatimLocality	minimumElevationInMeters	maximumElevationInMeters	verbatimElevation	minimumDepthInMeters	maximumDepthInMeters	locationRemarks	decimalLatitude	decimalLongitude	geodeticDatum	coordinateUncertaintyInMeters	verbatimLatitude	verbatimLongitude	verbatimCoordinateSystem	georeferencedBy	georeferenceProtocol	georeferenceSources	georeferenceRemarks	earliestEraOrLowestErathem	latestEraOrHighestErathem	earliestPeriodOrLowestSystem	latestPeriodOrHighestSystem	earliestEpochOrLowestSeries	latestEpochOrHighestSeries	earliestAgeOrLowestStage	latestAgeOrHighestStage	lithostratigraphicTerms	group	formation	member	bed	identificationQualifier	typeStatus	identifiedBy	identifiedByID	dateIdentified	identificationRemarks	taxonID	scientificNameID	scientificName	higherClassification	kingdom	phylum	class	order	family	genus	genericName	specificEpithet	infraspecificEpithet	taxonRank	verbatimTaxonRank	scientificNameAuthorship	nomenclaturalCode
MCZ:Herp:R-147033	2021-12-02 21:30:28	President and Fellows of Harvard College	http://mczbase.mcz.harvard.edu/guid/MCZ:Herp:R-147033	b4640710-8e03-11d8-b956-b8a03c50a862		MCZ	Herp	Museum of Comparative Zoology, Harvard University	PreservedSpecimen		{}	MCZ:Herp:R-147033	R-147033	MCZ FS-F20823	Kenneth I. Miyata		1			unverified	present	whole animal (ethanol)	unknown					collector number=MCZ FS-F20823; muse location number=ZR147033			1975-08-12	224	1975	08	12	12/8/1975-12/8/1975			http://vocab.getty.edu/tgn/1001487	South America: Ecuador: Pichincha	South America				Ecuador	EC	Pichincha		Ecuador: Pichincha: 41 km from Santo Domingo de los Colorados on rd to Quevedo	Ecuador: Pichincha Prov.: 41 km from Santo Domingo de los Colorados on rd to Quevedo							-0.53900391	-79.37394714	WGS84	3994			decimal degrees	Elisa Bonaccorso	MaNIS/HerpNET/ORNIS Georeferencing Guidelines	Map SA17-3 (Santo Domingo de los Colorados) map 1:250,000. IGM Ecuador																	Catalog						Anolis festae	Animalia Chordata Reptilia Lepidosauromorpha Squamata Sauria Iguanidae Anolis festae	Animalia	Chordata	Reptilia	Squamata	Iguanidae	Anolis	Anolis	festae					ICZN

Would align taxon name Anolis festae with Catalog of Life, resulting in output:

jhpoelen commented 2 years ago

@seltmann suggested to prepend the exact location of the row that the name was extracted from:

e.g.,

jhpoelen commented 2 years ago

suggest to use ucsb-izc as a smaller example to try out the concept, then move to MCZ to get a sense for the performance of the method.

globalbioticinteractions / mcz

Create a name report #3