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Plantminer

Match lists of taxa against the Brazilian Flora 2020 and The Plant List.

Online version

http://www.plantminer.com

Run a local version

install.packages("devtools")
devtools::install_github("gustavobio/tpldata")
devtools::install_github("gustavobio/tpl")
devtools::install_github("gustavobio/flora")
install.packages("shiny")
install.packages("DT")
install.packages("shinydashboard")
library("shiny")
download.file("https://raw.githubusercontent.com/gustavobio/plantminer/master/app.R", paste0(tempdir(), "app.R"))
runApp(paste0(tempdir(), "app.R"), launch.browser = TRUE)

API

Flora API call

Use the /flora method to GET request a taxon using the taxon querystring:

http://www.plantminer.com/flora?taxon=Coffea%20arabica The response is always a json object, even if there is no match.

Fields

#####id Taxon id in the Brazilian Flora Checklist.

#####scientific name Full name with authors

#####original search Character string supplied by the user and matched against the database.

#####search str Character string used internally to query the database. If the user entered a misspelled name and a suggestion could be made, this will not match the original search.

#####taxon status Taxonomical status. Possible values are as follows: accepted synonym

#####notes Notes about a taxon. Empty string if there is nothing to report. Otherwise, possible values are as follows:

not found, if a name was not found. was misspelled, if a name was misspelled. replaced synonym, if a name was a synonym and was replaced by an accepted name. check no accepted name if a synonym is not linked to a accepted name. check no accepted +1 synonyms if a supplied taxon matches several names listed as synonyms and none are linked to an accepted name. check +1 accepted if a synonym is linked to two or more accepted names. check +1 entries if a supplied taxon matches several entries in the database. check undefined status if a name is neither accepted or a synonym according to the data. Multiple notes are separated with a |

#####taxon rank Taxonomical rank of the user supplied taxon. Possible values are:

family genus species

#####family Taxon family according to the Brazilian Flora Checklist

#####threat status Taxon threat status according to CNC Flora 2013. Statuses follow the IUCN convention.

TPL API call

Use the /tpl method to GET request a taxon using the taxon querystring:

http://www.plantminer.com/tpl?taxon=Coffea%20arabica The response is always a json object, even if a match couldn't be made.

Fields

#####id Taxon id in The Plant List

#####family Taxon family according to The Plant List. There is an option to return APG families instead.

#####genus Taxon genus

#####species Specific epiteth

#####infraspecific rank Taxon infraspecific rank

#####infraspecific epithet Taxon infraspecific epithet

#####authorship Taxon author(s)

#####taxonomic status in tpl Taxon status according to The Plant List. Possible values are:

Accepted Synonym

#####confidence level Status confidence level. Possible values are: H: high confidence M: medium confidence L: low confidence

#####source Source of the data. Please check their website for a list of all possible sources and how to cite them.

#####accepted id id of the accepted name of a taxon in The Plant List. Return only if the user chooses not to automatically replace synonyms.

#####name Taxon name without authors.

#####note Notes about the taxon matching. Possible values are:

not found, if a name was not found. was misspelled, if a name was misspelled. replaced synonym, if a name is listed as a synonym and an accepted name was found. Multiple notes are separated with a |

#####original search The user supplied character string.

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Match lists of taxa against the Brazilian Flora Checklist and The Plant List

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