R语言【taxa】——df_ref()：有效的 分类信息数据库

Package taxa version 0.4.2

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Description

        定义可以被 taxon_db 对象使用或使用 taxon_db 对象的有效分类数据库，例如 taxon_id 和 taxon。

        使用 db_ref$get 查看数据库的详细信息。

        用户可以使用 db_ref$set 创建自定义的数据库，并添加到数据库列表中。

        每个数据库都必须包含下列信息：

• 数据库对应的网站的URL
• 一段简短的描述
• 定义有效的类群ID的正则表达式
• 数据库中有效的分类等级

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Usage

db_ref

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Format

一个长度为3的列表对象。

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Attribution

此代码基于knitr包中的代码处理选项。

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Examples

查看所有的数据库定义：

db_ref$get()

<taxon_db_def[8]>
   _____________________ ncbi ______________________
   url:         http://www.ncbi.nlm.nih.gov/taxonomy
   desc:        NCBI Taxonomy Database              
   id_regex:    [0-9]+                              
   rank_levels:                                     

   _____________________________ gbif _____________________________
   url:         http://www.gbif.org/developer/species              
   desc:        GBIF Taxonomic Backbone                            
   id_regex:    [0-9]+                                             
   rank_levels: kingdom < phylum < order < family < genus < species

   _____________________________________ bold _____________________________________
   url:         http://www.boldsystems.org                                         
   desc:        Barcode of Life                                                    
   id_regex:    [0-9]+                                                             
   rank_levels: phylum < class < order < family < subfamily < genus < species < su…

   ___________________ col ___________________
   url:         http://www.catalogueoflife.org
   desc:        Catalogue of Life             
   id_regex:    [a-z0-9]{32}                  
   rank_levels:                               

   ______________ eol ______________
   url:         http://eol.org      
   desc:        Encyclopedia of Life
   id_regex:    [0-9]+              
   rank_levels:                     

   ____________________ nbn ____________________
   url:         https://nbn.org.uk              
   desc:        UK National Biodiversity Network
   id_regex:    [A-Z]{5}[0-9]{10}               
   rank_levels:                                 

   ________________ tps ________________
   url:         http://www.tropicos.org/
   desc:        Tropicos                
   id_regex:    [0-9]+                  
   rank_levels:                         

   _______________________ itis _______________________
   url:         http://www.itis.gov                    
   desc:        Integrated Taxonomic Information System
   id_regex:    [0-9]+                                 
   rank_levels:                                        

自定义数据库：

db_ref$set(
  name = "my_new_database",
  url = "http://www.my_tax_database.com",
  desc = "I just made this up",
  id_regex = ".*"
)

db_ref$get()

<taxon_db_def[9]>
   _____________________ ncbi ______________________
   url:         http://www.ncbi.nlm.nih.gov/taxonomy
   desc:        NCBI Taxonomy Database              
   id_regex:    [0-9]+                              
   rank_levels:                                     

   _____________________________ gbif _____________________________
   url:         http://www.gbif.org/developer/species              
   desc:        GBIF Taxonomic Backbone                            
   id_regex:    [0-9]+                                             
   rank_levels: kingdom < phylum < order < family < genus < species

   ________________________________________ bold _________________________________________
   url:         http://www.boldsystems.org                                                
   desc:        Barcode of Life                                                           
   id_regex:    [0-9]+                                                                    
   rank_levels: phylum < class < order < family < subfamily < genus < species < subspecies

   ___________________ col ___________________    ______________ eol ______________
   url:         http://www.catalogueoflife.org    url:         http://eol.org      
   desc:        Catalogue of Life                 desc:        Encyclopedia of Life
   id_regex:    [a-z0-9]{32}                      id_regex:    [0-9]+              
   rank_levels:                                   rank_levels:                     

   ____________________ nbn ____________________    ________________ tps ________________
   url:         https://nbn.org.uk                  url:         http://www.tropicos.org/
   desc:        UK National Biodiversity Network    desc:        Tropicos                
   id_regex:    [A-Z]{5}[0-9]{10}                   id_regex:    [0-9]+                  
   rank_levels:                                     rank_levels:                         

   _______________________ itis _______________________    _____________ my_new_database _____________
   url:         http://www.itis.gov                        url:         http://www.my_tax_database.com
   desc:        Integrated Taxonomic Information System    desc:        I just made this up           
   id_regex:    [0-9]+                                     id_regex:    .*                            
   rank_levels:                                            rank_levels:                               

恢复默认设置：

db_ref$reset()

db_ref$get()

<taxon_db_def[8]>
   _____________________ ncbi ______________________
   url:         http://www.ncbi.nlm.nih.gov/taxonomy
   desc:        NCBI Taxonomy Database              
   id_regex:    [0-9]+                              
   rank_levels:                                     

   _____________________________ gbif _____________________________
   url:         http://www.gbif.org/developer/species              
   desc:        GBIF Taxonomic Backbone                            
   id_regex:    [0-9]+                                             
   rank_levels: kingdom < phylum < order < family < genus < species

   ________________________________________ bold _________________________________________
   url:         http://www.boldsystems.org                                                
   desc:        Barcode of Life                                                           
   id_regex:    [0-9]+                                                                    
   rank_levels: phylum < class < order < family < subfamily < genus < species < subspecies

   ___________________ col ___________________    ______________ eol ______________
   url:         http://www.catalogueoflife.org    url:         http://eol.org      
   desc:        Catalogue of Life                 desc:        Encyclopedia of Life
   id_regex:    [a-z0-9]{32}                      id_regex:    [0-9]+              
   rank_levels:                                   rank_levels:                     

   ____________________ nbn ____________________    ________________ tps ________________
   url:         https://nbn.org.uk                  url:         http://www.tropicos.org/
   desc:        UK National Biodiversity Network    desc:        Tropicos                
   id_regex:    [A-Z]{5}[0-9]{10}                   id_regex:    [0-9]+                  
   rank_levels:                                     rank_levels:                         

   _______________________ itis _______________________
   url:         http://www.itis.gov                    
   desc:        Integrated Taxonomic Information System
   id_regex:    [0-9]+                                 
   rank_levels: