Table 2.
Details on the chemical NER tools in terms of training sets, databases to which the entities are normalized, classes of chemicals addressed, and tokenization methods
| NER tool | Training set | Databases | Classes | Tokenization method |
|---|---|---|---|---|
| tmChem [24] | CHEMDNER corpus at BioCreative IV (training and development sets) | CHEBI | SYSTEMATIC | Tokenization at every non-letter and non-digit characters, number- letter changes and lower case letter followed by an uppercase letter |
| MESH | FORMULA | |||
| FAMILY | ||||
| TRIVIAL | ||||
| IDENTIFIER | ||||
| MULTIPLE | ||||
| ABBREVIATION | ||||
| ChemSpot [13] | A subset of SCAI Corpus [29] containing only IUPAC | ChemIDplus | SYSTEMATIC | Tokenization at every non-letter and non-digit characters and number-letter changes |
| CHEBI | FORMULA | |||
| CAS | FAMILY | |||
| NUMBER | TRIVIAL | |||
| PubChem | IDENTIFIER | |||
| InChI | MULTIPLE | |||
| DrugBank | ABBREVIATION | |||
| KEGG | ||||
| Human | ||||
| Metabolome | ||||
| MESH |