Framework for identifying biomedical entities
Dependencies and other uses should follow the original ReadMe.
This is a fork created to accomodate an annotator for the Human Phenotype Ontology. It uses Gold Standard Corpora and Test Suites Created by Bio-Lark. Link Here
If a corpus is to be loaded into IBEnt, it's necessary to run Stanford CoreNLP.
cd StanfordCoreNLP_Folder
java -mx4g -cp "*" edu.stanford.nlp.pipeline.StanfordCoreNLPServer -timeout 500000
##Load Corpus (For both Gold Standard Corpora and Test Suite)
python src/main.py load_corpus --goldstd hpo_train --log DEBUG
python src/main.py load_corpus --goldstd hpo_test --log DEBUG
python src/main.py load_corpus --goldstd tsuite --log DEBUG
##Train, Test and Evaluate with StanfordNER
python src/main.py train --goldstd hpo_train --models models/hpo_train --log DEBUG
python src/main.py test --goldstd hpo_test -o pickle data/results_hpo_train --models models/hpo_train --log DEBUG
python src/evaluate.py evaluate hpo_test --results data/results_hpo_train --models models/hpo_train --log DEBUG
##Train, Test and Evaluate with CRFSuite
python src/main.py train --goldstd hpo_train --models models/hpo_train --log DEBUG --entitytype hpo --crf crfsuite
python src/main.py test --goldstd hpo_test -o pickle data/results_hpo_train --models models/hpo_train --log DEBUG --entitytype hpo --crf crfsuite
python src/evaluate.py evaluate hpo_test --results data/results_hpo_train --models models/hpo_train --log DEBUG --entitytype hpo
##Test and Evaluate for Test Suites
python src/main.py test --goldstd tsuite -o pickle data/results_hpo_train --models models/hpo_train --log DEBUG --entitytype hpo --crf crfsuite
python src/evaluate.py evaluate tsuite --results data/results_hpo_train --models models/hpo_train --log DEBUG --entitytype hpo
Rules can be added to the evaluation parameters:
--rules andor stopwords small_ent twice_validated stopwords gowords posgowords longterms small_len quotes defwords digits lastwords