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Access Terms From the Plant Phenology Ontology

Source: R/ppo_get_terms.R
ppo_get_terms.Rd

Access present and absent terms from the Plant Phenology Ontology

Usage

ppo_get_terms(present = FALSE, absent = FALSE)

Arguments

present

(boolean) If TRUE then return all "present" phenological stages

absent

(boolean) IF TRUE then return all "absent" phenological stages.

Value

A data frame with the columns: termID, label, description, and URI.

Details

The ppo_terms function returns terms from the Plant Phenology Ontology (PPO). The termID or label column can be used to query the `termID` or `mapped_traits` to ppo_data. The label and description columns are useful in determining the trait to query on. The URI column contains a link to the term itself which is useful for determining superclass and subclass relationships for each term.

Examples

presentTerms <- ppo_terms(present = TRUE)
#> sending request for data ...
#> https://biscicol.org/api/v1/ppo/present/
#> The server encountered an issue processing your
#>              request and returned status code =  502 . If the problem persists contact the author.
absentTerms <- ppo_terms(absent = TRUE)
#> sending request for data ...
#> https://biscicol.org/api/v1/ppo/absent/
#> The server encountered an issue processing your
#>              request and returned status code =  502 . If the problem persists contact the author.
allTerms <- ppo_terms(present = TRUE, absent = TRUE)
#> sending request for data ...
#> https://biscicol.org/api/v1/ppo/all/
#> The server encountered an issue processing your
#>              request and returned status code =  502 . If the problem persists contact the author.
fruitTerms <- grep("fruit", ppo_filters$mapped_traits$label, value = TRUE)
ppo_data(genus = c( "Pinus", "Quercus"),
         specificEpithet = "palustris",
         mapped_traits = fruitTerms,
         fromYear = 2016, toYear = 2017)
#> sending request for data ...
#> https://biscicol.org/api/v3/download/_search?q=+genus:("Pinus","Quercus")++AND+++specificEpithet:palustris++AND+++year:>=2016++AND+++year:<=2017++AND+++mapped_traits:("abscised+fruits+or+seeds+absent","abscised+fruits+or+seeds+present","fruits+present","ripe+fruits+absent","ripe+fruits+present","ripening+fruits+absent","ripening+fruits+present","unripe+fruits+absent")&limit=100000
#> The server encountered an issue processing your
#>              request and returned status code =  502 . If the problem persists contact the author.
#> $data
#> NULL
#> 
#> $readme
#> NULL
#> 
#> $citation
#> NULL
#> 
#> $number_possible
#> [1] 0
#> 
#> $status_code
#> [1] 502
#>