NCBI disease corpus - related resources
Original data available from http://www.ncbi.nlm.nih.gov/CBBresearch/Dogan/DISEASE/
python tools/ncbidisease2ann.py original-data/train/NCBItrainset_corpus.txt standoff/train
python tools/ncbidisease2ann.py original-data/devel/NCBIdevelopset_corpus.txt standoff/devel
python tools/ncbidisease2ann.py original-data/test/NCBItestset_corpus.txt standoff/test
Note: there is a duplicate document (PMID 8528200) in the original
data, and the duplicate is recreated in the converted data by default.
Run with -dedup to eliminate the duplicate.
(See #1)
git clone git@github.com:spyysalo/standoff2conll.git
for i in train devel test; do
python standoff2conll/standoff2conll.py -1 Disease standoff/$i > conll/$i.tsv
done
for i in train devel test; do
python tools/conll2crfsuite.py < conll/$i.tsv > crfsuite/$i.crfsuite
done