Data associated with the S1000 corpus The tagger software for which the dictionary files in tagger-organisms-dictionary-S1000.tar.gz can be used with can be found here: https://github.com/larsjuhljensen/tagger The online version of the annotation documentation can be found here: https://katnastou.github.io/s1000-corpus-annotation-guidelines/ The S1000 corpus split in training, development and test sets in BRAT format can be found in S1000-corpus.tar.gz and in CoNLL format here: s1000-conll.tar.gz The tagging results of Jensenlab tagger for the S1000 test set are here: S1000-jensenlab-tagger.tar.gz The result from the large scale run in entire PubMed and PMC Open Access articles for Jensenlab tagger is provided here: Jensenlab_tagger_large_scale_matches_with_rank.tsv.gz The model used for the large scale run of the transformer-based method is here: S1000_Transformer_based_tagger_large_scale_model.tar.gz and the results from the large scale tagging here: Transformer_based_tagger_large_scale_matches_with_rank.tsv.zip