FoodMapr

This is a derived work from LexMapr that focuses on food items and products.

What are the differences:

Include the English stop words as the default.
Remove the functionalities to output the text buckets and classifications.
Remove the micro and macro match statuses.
Introduce a new profile called "anz" to map the Australia New Zealand Food Standards to the Food Ontology concepts.
```
$ foodmapr input.csv -p anz -o output.json
```

Installation

Install Conda.
Create a FoodMapr environment
```
$ conda create --name FoodMapr
```

Install FoodMapr into your conda environment:

$ conda activate FoodMapr
$ git clone https://github.com/johardi/FoodMapr.git
$ cd FoodMapr
$ pip install .
$ python -m nltk.downloader punkt
$ python -m nltk.downloader stopwords

(Optional) Set an environment variable USER_NLTK_DATA for a user-defined NLTK data location
```
$ export USER_NLTK_DATA=/path/to/nltk_data
```
Alternatively, edit .bash_profile and add the environment variable to make it available at startup

Usage

Prepare the input file: food.csv

FoodId,FoodName
F001,Chicken Breast
F002,Baked Potato
F003,Canned Corn
F004,Frozen Yogurt
F005,Apple Pie

Prepare the configuration file: config_foodon.json

[
   { "http://purl.obolibrary.org/obo/foodon.owl": [
        "http://purl.obolibrary.org/obo/FOODON_00001871",
        "http://purl.obolibrary.org/obo/FOODON_00002373",
        "http://purl.obolibrary.org/obo/FOODON_00002381",
        "http://purl.obolibrary.org/obo/FOODON_00002645",
        "http://purl.obolibrary.org/obo/FOODON_00001180",
        "http://purl.obolibrary.org/obo/FOODON_03311737",
        "http://purl.obolibrary.org/obo/FOODON_00001714"
     ]
   }
]

Run the command on the Terminal console

(FoodMapr) foo@bar:~$ foodmapr food.csv -c config_foodon.json
{
   "mapping_output": {
      "Chicken Breast:F001": "chicken breast:FOODON_00002703",
      "Baked Potato:F002": "potato (whole, baked):FOODON_03302196",
      "Canned Corn:F003": "corn (canned):FOODON_03302665",
      "Frozen Yogurt:F004": "frozen yogurt:FOODON_03307445",
      "Apple Pie:F005": "apple pie:FOODON_00002475"
   },
   "input_to_ontology_mapping": {
      "F001": "FOODON_00002703",
      "F002": "FOODON_03302196",
      "F003": "FOODON_03302665",
      "F004": "FOODON_03307445",
      "F005": "FOODON_00002475"
   },
   "ontology_to_input_mapping": {
      "FOODON_00002703": "F001",
      "FOODON_03302196": "F002",
      "FOODON_03302665": "F003",
      "FOODON_03307445": "F004",
      "FOODON_00002475": "F005"
   },
   "input_term_label": {
      "F001": "Chicken Breast",
      "F002": "Baked Potato",
      "F003": "Canned Corn",
      "F004": "Frozen Yogurt",
      "F005": "Apple Pie"
   },
   "ontology_term_label": {
      "FOODON_00002703": "chicken breast",
      "FOODON_03302196": "potato (whole, baked)",
      "FOODON_03302665": "corn (canned)",
      "FOODON_03307445": "frozen yogurt",
      "FOODON_00002475": "apple pie"
   }
}

johardi/FoodMapr

FoodMapr

Installation

Usage

More Documentation from LexMapr