Table 1.
Benchmark Corpora used for analyzing BioNER systems.
| Corpus | Year | Text type | Training data type | Data size |
|---|---|---|---|---|
| ChEBI (Shardlow et al., 2018) | 2018 | Abstracts/Full text | Chemical Entities of Biological Interest | Abs-199/FT-100 (15,000 mentions) |
| CHEMDNER (Krallinger et al., 2015) | 2015 | Pubmed Abstracts | Chemicals and Drugs | 10,000 (84,355 Entity mentions) |
| NCBI Disease (Dogan et al., 2014) | 2014 | Pubmed Abstracts | Diseases | 793 (6,892 Disease mentions) |
| CRAFT (Bada et al., 2012) | 2012 | Full Text | Cell Type, Chemical Entities of Biological Interest, NCBI Taxonomy, protein, Sequence, Gene, DNA, RNA | 97 (140,000 Annotations) |
| AnEM (Ohta et al., 2012) | 2012 | Abstracts/ Full text | Pathology, Anatomical Structures/Substances | 500 (3,000 mentions) |
| NaCTeM Metabolite and Enzyme (Nobata et al., 2011) | 2011 | Medline Abstracts | Metabolites and Enzymes | 296 |
| LINNAEUS (Gerner et al., 2010) | 2010 | Full text Documents | Species | 100 |
| GENETAG (Tanabe et al., 2005) | 2005 | Sentences | Gene, Protein | 20,000 Sentences |
| JNLPBA (Huang et al., 2019) | 2004 | Abstracts | DNA, RNA, Protein, Cell Type, Cell Line | 2,000 (+404 testset) |
| GENIA (Kim et al., 2003) | 2003 | Pubmed Abstracts | DNA, RNA, Protein, Cells, Tissue, Anatomy, Organisms, Chemicals | 2,000 |