Mapping samples against an entire ontology

example_config_all_foodon.json:

[
  {
    "http://purl.obolibrary.org/obo/foodon.owl": 
    "http://purl.obolibrary.org/obo/BFO_0000001"
  }
]

example_input.csv:

id,sample
0,potato flakes
1,fish fillet
2,wheat

Run:

$ lexmapr example_input.csv -c example_config_all_fooodon.json

Terminal output:

Sample_Id       Sample_Desc     Cleaned_Sample  Matched_Components
0       potato flakes   potato flakes   ['potato flakes:foodon_00002792']
1       fish fillet     fish fillet     ['fish fillet:foodon_00002679']
2       wheat   wheat   ['wheat:foodon_03315184']

Mapping samples against a subset of an ontology

example_config_foodon_plants_only.json:

[
  {
    "http://purl.obolibrary.org/obo/foodon.owl": 
    "http://purl.obolibrary.org/obo/FOODON_00001015"
  }
]

example_input.csv

id,sample
0,potato flakes
1,fish fillet
2,wheat

Run:

$ lexmapr example_input.csv -c example_config_foodon_plants_only.json

Terminal output:

0       potato flakes   potato flakes   ['potato flakes:foodon_00002792']
1       fish fillet     fish fillet     []
2       wheat   wheat   ['wheat:foodon_03315184']

Mapping samples against multiple ontologies

example_config_foodon_and_envo.json:

[
  {
    "http://purl.obolibrary.org/obo/foodon.owl": 
    "http://purl.obolibrary.org/obo/BFO_0000001"
  },
  {
    "http://purl.obolibrary.org/obo/envo.owl": 
    "http://purl.obolibrary.org/obo/BFO_0000001"
  }
]

example_input.csv

id,sample
0,potato flakes from a field
1,fish fillet from a lake
2,wheat from a mountain

Run:

$ lexmapr example_input.csv -c example_config_foodon_and_envo.json

Terminal output:

Sample_Id       Sample_Desc     Cleaned_Sample  Matched_Components
0       potato flakes from a field      potato flakes field     ['potato flakes:foodon_00002792', 'field:envo_01000352']
1       fish fillet from a lake fish fillet lake        ['fish fillet:foodon_00002679', 'lake:envo_00000020']
2       wheat from a mountain   wheat mountain  ['wheat:foodon_03315184', 'mountain:envo_00000081']