A Lexicon and Rule-Based Tool for Translating Short Biomedical Specimen Descriptions into Semantic Web Ontology Terms
Set up Bioconda, if you haven't already!
Then:
$ conda create -n LexMapr lexmapr python=3.11
$ conda activate LexMapr
$ python -m nltk.downloader all
Install Conda.
Create a LexMapr environment:
$ conda create --name LexMapr python=3.11
(Python 3.11+ at moment doesn't work due to some core module changes).
Install LexMapr into your conda environment:
$ conda activate LexMapr
$ git clone https://github.com/cidgoh/LexMapr.git
$ cd LexMapr
$ pip install .
$ python -m nltk.downloader all
small_simple.csv
SampleId,Sample
small_simple1,Chicken Breast
small_simple2,Baked Potato
small_simple3,Canned Corn
small_simple4,Frozen Yogurt
small_simple5,Apple Pie
small_simple_config.json
[
{"http://purl.obolibrary.org/obo/foodon.owl": "http://purl.obolibrary.org/obo/BFO_0000040"},
{"http://purl.obolibrary.org/obo/foodon.owl": "http://purl.obolibrary.org/obo/BFO_0000015"}
](LexMapr) foo@bar:~$ lexmapr small_simple.csv -c small_simple_config.json
Sample_Id Sample_Desc Cleaned_Sample Matched_Components
small_simple1 Chicken Breast chicken breast ['chicken breast:foodon_00002703']
small_simple2 Baked Potato baked potato ['potato (whole, baked):foodon_03302196']
small_simple3 Canned Corn canned corn ['corn (canned):foodon_03302665']
small_simple4 Frozen Yogurt frozen yogurt ['frozen yogurt:foodon_03307445']
small_simple5 Apple Pie apple pie ['apple pie:foodon_00002475']Tutorial slides for users with little or no experience with command line
Tutorial slides for IFSAC users with little or no experience with command line